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https://www.piwheels.org/simple/janis-pipelines-core/janis_pipelines.core-0.4.0-py3-none-any.whl#sha256=98c1fc45d6e06c87373bb7c7e0999fbc9a1881427808eb5dc9260a45ed805efd (from https://www.piwheels.org/simple/janis-pipelines-core/) 2023-09-27T07:48:09,039 Skipping link: not a file: https://www.piwheels.org/simple/janis-pipelines-core/ 2023-09-27T07:48:09,040 Skipping link: not a file: https://pypi.org/simple/janis-pipelines-core/ 2023-09-27T07:48:09,065 Given no hashes to check 1 links for project 'janis-pipelines-core': discarding no candidates 2023-09-27T07:48:09,083 Collecting janis-pipelines-core==0.13.1 2023-09-27T07:48:09,086 Created temporary directory: /tmp/pip-unpack-cvkz6qey 2023-09-27T07:48:09,562 Downloading janis-pipelines.core-0.13.1.tar.gz (73.2 MB) 2023-09-27T07:48:34,757 Added janis-pipelines-core==0.13.1 from https://files.pythonhosted.org/packages/0f/83/9dd041902176b2edae4c94076e7b51400a98c034b0518cef149b0fbc13f4/janis-pipelines.core-0.13.1.tar.gz to build tracker '/tmp/pip-build-tracker-p669mipu' 2023-09-27T07:48:34,763 Created temporary directory: /tmp/pip-build-env-rwc1kdsn 2023-09-27T07:48:34,767 Installing build dependencies: started 2023-09-27T07:48:34,769 Running command pip subprocess to install build dependencies 2023-09-27T07:48:36,052 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-27T07:48:36,602 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-27T07:48:38,146 Collecting setuptools>=67.8.0 2023-09-27T07:48:38,147 Obtaining dependency information for setuptools>=67.8.0 from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata 2023-09-27T07:48:38,153 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-27T07:48:38,360 Collecting wheel>=0.40.0 2023-09-27T07:48:38,375 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-27T07:48:38,550 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-27T07:48:41,017 Installing collected packages: wheel, setuptools 2023-09-27T07:48:41,250 Creating /tmp/pip-build-env-rwc1kdsn/overlay/local/bin 2023-09-27T07:48:41,252 changing mode of /tmp/pip-build-env-rwc1kdsn/overlay/local/bin/wheel to 755 2023-09-27T07:48:43,553 Successfully installed setuptools-68.2.2 wheel-0.41.2 2023-09-27T07:48:44,135 Installing build dependencies: finished with status 'done' 2023-09-27T07:48:44,140 Getting requirements to build wheel: started 2023-09-27T07:48:44,142 Running command Getting requirements to build wheel 2023-09-27T07:48:45,284 running egg_info 2023-09-27T07:48:45,288 writing janis_pipelines.core.egg-info/PKG-INFO 2023-09-27T07:48:45,293 writing dependency_links to janis_pipelines.core.egg-info/dependency_links.txt 2023-09-27T07:48:45,296 writing requirements to janis_pipelines.core.egg-info/requires.txt 2023-09-27T07:48:45,297 writing top-level names to janis_pipelines.core.egg-info/top_level.txt 2023-09-27T07:48:45,378 reading manifest file 'janis_pipelines.core.egg-info/SOURCES.txt' 2023-09-27T07:48:45,632 adding license file 'LICENSE' 2023-09-27T07:48:45,715 writing manifest file 'janis_pipelines.core.egg-info/SOURCES.txt' 2023-09-27T07:48:45,837 Getting requirements to build wheel: finished with status 'done' 2023-09-27T07:48:45,846 Created temporary directory: /tmp/pip-modern-metadata-h0shqawk 2023-09-27T07:48:45,848 Preparing metadata (pyproject.toml): started 2023-09-27T07:48:45,849 Running command Preparing metadata (pyproject.toml) 2023-09-27T07:48:46,874 running dist_info 2023-09-27T07:48:46,879 creating /tmp/pip-modern-metadata-h0shqawk/janis_pipelines.core.egg-info 2023-09-27T07:48:46,884 writing /tmp/pip-modern-metadata-h0shqawk/janis_pipelines.core.egg-info/PKG-INFO 2023-09-27T07:48:46,889 writing dependency_links to /tmp/pip-modern-metadata-h0shqawk/janis_pipelines.core.egg-info/dependency_links.txt 2023-09-27T07:48:46,892 writing requirements to /tmp/pip-modern-metadata-h0shqawk/janis_pipelines.core.egg-info/requires.txt 2023-09-27T07:48:46,893 writing top-level names to /tmp/pip-modern-metadata-h0shqawk/janis_pipelines.core.egg-info/top_level.txt 2023-09-27T07:48:46,894 writing manifest file '/tmp/pip-modern-metadata-h0shqawk/janis_pipelines.core.egg-info/SOURCES.txt' 2023-09-27T07:48:46,970 reading manifest file '/tmp/pip-modern-metadata-h0shqawk/janis_pipelines.core.egg-info/SOURCES.txt' 2023-09-27T07:48:46,972 adding license file 'LICENSE' 2023-09-27T07:48:46,990 writing manifest file '/tmp/pip-modern-metadata-h0shqawk/janis_pipelines.core.egg-info/SOURCES.txt' 2023-09-27T07:48:46,992 creating '/tmp/pip-modern-metadata-h0shqawk/janis_pipelines.core-0.13.1.dist-info' 2023-09-27T07:48:47,149 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-27T07:48:47,161 Source in /tmp/pip-wheel-ptp037c5/janis-pipelines-core_9ed3b481be7b4e3597afd984f2d7cde2 has version 0.13.1, which satisfies requirement janis-pipelines-core==0.13.1 from https://files.pythonhosted.org/packages/0f/83/9dd041902176b2edae4c94076e7b51400a98c034b0518cef149b0fbc13f4/janis-pipelines.core-0.13.1.tar.gz 2023-09-27T07:48:47,162 Removed janis-pipelines-core==0.13.1 from https://files.pythonhosted.org/packages/0f/83/9dd041902176b2edae4c94076e7b51400a98c034b0518cef149b0fbc13f4/janis-pipelines.core-0.13.1.tar.gz from build tracker '/tmp/pip-build-tracker-p669mipu' 2023-09-27T07:48:47,181 Created temporary directory: /tmp/pip-unpack-sp2h3ls8 2023-09-27T07:48:47,182 Created temporary directory: /tmp/pip-unpack-soppnd_e 2023-09-27T07:48:47,231 Building wheels for collected packages: janis-pipelines-core 2023-09-27T07:48:47,236 Created temporary directory: /tmp/pip-wheel-bvvu18yt 2023-09-27T07:48:47,236 Destination directory: /tmp/pip-wheel-bvvu18yt 2023-09-27T07:48:47,239 Building wheel for janis-pipelines-core (pyproject.toml): started 2023-09-27T07:48:47,240 Running command Building wheel for janis-pipelines-core (pyproject.toml) 2023-09-27T07:48:48,071 running bdist_wheel 2023-09-27T07:48:48,088 running build 2023-09-27T07:48:48,089 running build_py 2023-09-27T07:48:48,093 creating build 2023-09-27T07:48:48,094 creating build/lib 2023-09-27T07:48:48,095 creating build/lib/janis_core 2023-09-27T07:48:48,096 copying janis_core/__meta__.py -> build/lib/janis_core 2023-09-27T07:48:48,098 copying janis_core/__init__.py -> build/lib/janis_core 2023-09-27T07:48:48,100 creating build/lib/janis_core/ingestion 2023-09-27T07:48:48,101 copying janis_core/ingestion/main.py -> build/lib/janis_core/ingestion 2023-09-27T07:48:48,103 copying janis_core/ingestion/SupportedIngestion.py -> build/lib/janis_core/ingestion 2023-09-27T07:48:48,105 copying janis_core/ingestion/__init__.py -> build/lib/janis_core/ingestion 2023-09-27T07:48:48,108 creating build/lib/janis_core/tests 2023-09-27T07:48:48,109 copying janis_core/tests/test_janis_translate.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,112 copying janis_core/tests/test_tools.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,114 copying janis_core/tests/test_validateinputvalue.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,116 copying janis_core/tests/test_logger.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,117 copying janis_core/tests/test_operators.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,119 copying janis_core/tests/test_translation_modules.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,121 copying janis_core/tests/test_receivefrom.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,123 copying janis_core/tests/test_test_runner.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,126 copying janis_core/tests/test_metadata.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,127 copying janis_core/tests/test_workflow.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,130 copying janis_core/tests/test_commandtool.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,131 copying janis_core/tests/test_translation_cwl.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,134 copying janis_core/tests/tests_util.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,136 copying janis_core/tests/test_validators.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,137 copying janis_core/tests/test_conditionals.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,139 copying janis_core/tests/test_stringbuilder.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,141 copying janis_core/tests/test_types.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,143 copying janis_core/tests/test_running.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,144 copying janis_core/tests/test_ingestion_wdl.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,146 copying janis_core/tests/__init__.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,147 copying janis_core/tests/test_step.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,149 copying janis_core/tests/test_ingestion_galaxy.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,152 copying janis_core/tests/test_translation_wdl.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,155 copying janis_core/tests/test_secondary.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,157 copying janis_core/tests/test_python_tool.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,159 copying janis_core/tests/test_translation_nextflow.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,163 copying janis_core/tests/test_generics_util.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,165 copying janis_core/tests/test_ingestion_cwl.py -> build/lib/janis_core/tests 2023-09-27T07:48:48,168 creating build/lib/janis_core/settings 2023-09-27T07:48:48,169 copying janis_core/settings/graph.py -> build/lib/janis_core/settings 2023-09-27T07:48:48,171 copying janis_core/settings/testing.py -> build/lib/janis_core/settings 2023-09-27T07:48:48,172 copying janis_core/settings/__init__.py -> build/lib/janis_core/settings 2023-09-27T07:48:48,174 copying janis_core/settings/validation.py -> build/lib/janis_core/settings 2023-09-27T07:48:48,176 copying janis_core/settings/datatypes.py -> build/lib/janis_core/settings 2023-09-27T07:48:48,178 creating build/lib/janis_core/tool 2023-09-27T07:48:48,179 copying janis_core/tool/tool.py -> build/lib/janis_core/tool 2023-09-27T07:48:48,181 copying janis_core/tool/test_suite_runner.py -> build/lib/janis_core/tool 2023-09-27T07:48:48,184 copying janis_core/tool/test_classes.py -> build/lib/janis_core/tool 2023-09-27T07:48:48,186 copying janis_core/tool/test_definitions.py -> build/lib/janis_core/tool 2023-09-27T07:48:48,188 copying janis_core/tool/batchrun.py -> build/lib/janis_core/tool 2023-09-27T07:48:48,190 copying janis_core/tool/cwl_tool_parser.py -> build/lib/janis_core/tool 2023-09-27T07:48:48,192 copying janis_core/tool/documentation.py -> build/lib/janis_core/tool 2023-09-27T07:48:48,194 copying janis_core/tool/__init__.py -> build/lib/janis_core/tool 2023-09-27T07:48:48,195 copying janis_core/tool/commandtool.py -> build/lib/janis_core/tool 2023-09-27T07:48:48,197 copying janis_core/tool/test_helpers.py -> build/lib/janis_core/tool 2023-09-27T07:48:48,200 creating build/lib/janis_core/hints 2023-09-27T07:48:48,201 copying janis_core/hints/__init__.py -> build/lib/janis_core/hints 2023-09-27T07:48:48,203 creating build/lib/janis_core/translation_deps 2023-09-27T07:48:48,204 copying janis_core/translation_deps/exportpath.py -> build/lib/janis_core/translation_deps 2023-09-27T07:48:48,205 copying janis_core/translation_deps/supportedtranslations.py -> build/lib/janis_core/translation_deps 2023-09-27T07:48:48,207 copying janis_core/translation_deps/__init__.py -> build/lib/janis_core/translation_deps 2023-09-27T07:48:48,209 creating build/lib/janis_core/code 2023-09-27T07:48:48,209 copying janis_core/code/codetool.py -> build/lib/janis_core/code 2023-09-27T07:48:48,211 copying janis_core/code/__init__.py -> build/lib/janis_core/code 2023-09-27T07:48:48,213 copying janis_core/code/pythontool.py -> build/lib/janis_core/code 2023-09-27T07:48:48,215 creating build/lib/janis_core/types 2023-09-27T07:48:48,216 copying janis_core/types/data_types.py -> build/lib/janis_core/types 2023-09-27T07:48:48,218 copying janis_core/types/common_data_types.py -> build/lib/janis_core/types 2023-09-27T07:48:48,220 copying janis_core/types/__init__.py -> build/lib/janis_core/types 2023-09-27T07:48:48,223 creating build/lib/janis_core/translation_utils 2023-09-27T07:48:48,224 copying janis_core/translation_utils/graph.py -> build/lib/janis_core/translation_utils 2023-09-27T07:48:48,225 copying janis_core/translation_utils/__init__.py -> build/lib/janis_core/translation_utils 2023-09-27T07:48:48,227 copying janis_core/translation_utils/datatypes.py -> build/lib/janis_core/translation_utils 2023-09-27T07:48:48,229 creating build/lib/janis_core/redefinitions 2023-09-27T07:48:48,230 copying janis_core/redefinitions/types.py -> build/lib/janis_core/redefinitions 2023-09-27T07:48:48,233 copying janis_core/redefinitions/__init__.py -> build/lib/janis_core/redefinitions 2023-09-27T07:48:48,235 copying janis_core/redefinitions/utils.py -> build/lib/janis_core/redefinitions 2023-09-27T07:48:48,237 creating build/lib/janis_core/transformation 2023-09-27T07:48:48,238 copying janis_core/transformation/__init__.py -> build/lib/janis_core/transformation 2023-09-27T07:48:48,240 creating build/lib/janis_core/workflow 2023-09-27T07:48:48,242 copying janis_core/workflow/__init__.py -> build/lib/janis_core/workflow 2023-09-27T07:48:48,243 copying janis_core/workflow/workflow.py -> build/lib/janis_core/workflow 2023-09-27T07:48:48,247 creating build/lib/janis_core/toolbox 2023-09-27T07:48:48,248 copying janis_core/toolbox/register.py -> build/lib/janis_core/toolbox 2023-09-27T07:48:48,251 copying janis_core/toolbox/toolbox.py -> build/lib/janis_core/toolbox 2023-09-27T07:48:48,253 copying janis_core/toolbox/entrypoints.py -> build/lib/janis_core/toolbox 2023-09-27T07:48:48,255 copying janis_core/toolbox/__init__.py -> build/lib/janis_core/toolbox 2023-09-27T07:48:48,257 creating build/lib/janis_core/graph 2023-09-27T07:48:48,258 copying janis_core/graph/steptaginput.py -> build/lib/janis_core/graph 2023-09-27T07:48:48,260 copying janis_core/graph/node.py -> build/lib/janis_core/graph 2023-09-27T07:48:48,262 copying janis_core/graph/__init__.py -> build/lib/janis_core/graph 2023-09-27T07:48:48,264 creating build/lib/janis_core/translations 2023-09-27T07:48:48,265 copying janis_core/translations/main.py -> build/lib/janis_core/translations 2023-09-27T07:48:48,268 copying janis_core/translations/translationbase.py -> build/lib/janis_core/translations 2023-09-27T07:48:48,270 copying janis_core/translations/__init__.py -> build/lib/janis_core/translations 2023-09-27T07:48:48,273 creating build/lib/janis_core/utils 2023-09-27T07:48:48,274 copying janis_core/utils/metadata.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,275 copying janis_core/utils/bracketmatching.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,277 copying janis_core/utils/pickvalue.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,279 copying janis_core/utils/errors.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,280 copying janis_core/utils/levenshteindistance.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,282 copying janis_core/utils/docparser_info.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,283 copying janis_core/utils/scatter.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,285 copying janis_core/utils/secondary.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,287 copying janis_core/utils/generators.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,288 copying janis_core/utils/yaml_utils.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,290 copying janis_core/utils/janisconstants.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,291 copying janis_core/utils/__init__.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,293 copying janis_core/utils/logger.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,295 copying janis_core/utils/validators.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,297 copying janis_core/utils/generics_util.py -> build/lib/janis_core/utils 2023-09-27T07:48:48,299 creating build/lib/janis_core/messages 2023-09-27T07:48:48,300 copying janis_core/messages/main.py -> build/lib/janis_core/messages 2023-09-27T07:48:48,302 copying janis_core/messages/logfile.py -> build/lib/janis_core/messages 2023-09-27T07:48:48,303 copying janis_core/messages/__init__.py -> build/lib/janis_core/messages 2023-09-27T07:48:48,306 creating build/lib/janis_core/operators 2023-09-27T07:48:48,306 copying janis_core/operators/selectors.py -> build/lib/janis_core/operators 2023-09-27T07:48:48,309 copying janis_core/operators/logical.py -> build/lib/janis_core/operators 2023-09-27T07:48:48,311 copying janis_core/operators/operator.py -> build/lib/janis_core/operators 2023-09-27T07:48:48,313 copying janis_core/operators/standard.py -> build/lib/janis_core/operators 2023-09-27T07:48:48,316 copying janis_core/operators/__init__.py -> build/lib/janis_core/operators 2023-09-27T07:48:48,317 copying janis_core/operators/stringformatter.py -> build/lib/janis_core/operators 2023-09-27T07:48:48,320 creating build/lib/janis_core/ingestion/cwl 2023-09-27T07:48:48,321 copying janis_core/ingestion/cwl/identifiers.py -> build/lib/janis_core/ingestion/cwl 2023-09-27T07:48:48,323 copying janis_core/ingestion/cwl/expressions.py -> build/lib/janis_core/ingestion/cwl 2023-09-27T07:48:48,325 copying janis_core/ingestion/cwl/main.py -> build/lib/janis_core/ingestion/cwl 2023-09-27T07:48:48,327 copying janis_core/ingestion/cwl/graph.py -> build/lib/janis_core/ingestion/cwl 2023-09-27T07:48:48,329 copying janis_core/ingestion/cwl/types.py -> build/lib/janis_core/ingestion/cwl 2023-09-27T07:48:48,331 copying janis_core/ingestion/cwl/preprocessing.py -> build/lib/janis_core/ingestion/cwl 2023-09-27T07:48:48,334 copying janis_core/ingestion/cwl/__init__.py -> build/lib/janis_core/ingestion/cwl 2023-09-27T07:48:48,335 copying janis_core/ingestion/cwl/loading.py -> build/lib/janis_core/ingestion/cwl 2023-09-27T07:48:48,338 creating build/lib/janis_core/ingestion/wdl 2023-09-27T07:48:48,339 copying janis_core/ingestion/wdl/main.py -> build/lib/janis_core/ingestion/wdl 2023-09-27T07:48:48,341 copying janis_core/ingestion/wdl/__init__.py -> build/lib/janis_core/ingestion/wdl 2023-09-27T07:48:48,344 creating build/lib/janis_core/ingestion/galaxy 2023-09-27T07:48:48,345 copying janis_core/ingestion/galaxy/aliases.py -> build/lib/janis_core/ingestion/galaxy 2023-09-27T07:48:48,346 copying janis_core/ingestion/galaxy/logging.py -> build/lib/janis_core/ingestion/galaxy 2023-09-27T07:48:48,348 copying janis_core/ingestion/galaxy/ingest.py -> build/lib/janis_core/ingestion/galaxy 2023-09-27T07:48:48,350 copying janis_core/ingestion/galaxy/__init__.py -> build/lib/janis_core/ingestion/galaxy 2023-09-27T07:48:48,352 creating build/lib/janis_core/ingestion/cwl/parsing 2023-09-27T07:48:48,353 copying janis_core/ingestion/cwl/parsing/tool.py -> build/lib/janis_core/ingestion/cwl/parsing 2023-09-27T07:48:48,357 copying janis_core/ingestion/cwl/parsing/__init__.py -> build/lib/janis_core/ingestion/cwl/parsing 2023-09-27T07:48:48,358 copying janis_core/ingestion/cwl/parsing/workflow.py -> build/lib/janis_core/ingestion/cwl/parsing 2023-09-27T07:48:48,361 creating build/lib/janis_core/ingestion/galaxy/gxworkflow 2023-09-27T07:48:48,361 copying janis_core/ingestion/galaxy/gxworkflow/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow 2023-09-27T07:48:48,364 creating build/lib/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:48,364 copying janis_core/ingestion/galaxy/datatypes/main.py -> build/lib/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:48,366 copying janis_core/ingestion/galaxy/datatypes/core.py -> build/lib/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:48,368 copying janis_core/ingestion/galaxy/datatypes/register.py -> build/lib/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:48,370 copying janis_core/ingestion/galaxy/datatypes/galaxy.py -> build/lib/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:48,374 copying janis_core/ingestion/galaxy/datatypes/JanisDatatype.py -> build/lib/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:48,375 copying janis_core/ingestion/galaxy/datatypes/__init__.py -> build/lib/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:48,377 copying janis_core/ingestion/galaxy/datatypes/conversion.py -> build/lib/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:48,378 copying janis_core/ingestion/galaxy/datatypes/strategies.py -> build/lib/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:48,381 creating build/lib/janis_core/ingestion/galaxy/gxwrappers 2023-09-27T07:48:48,382 copying janis_core/ingestion/galaxy/gxwrappers/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers 2023-09-27T07:48:48,384 creating build/lib/janis_core/ingestion/galaxy/janis_mapping 2023-09-27T07:48:48,385 copying janis_core/ingestion/galaxy/janis_mapping/general.py -> build/lib/janis_core/ingestion/galaxy/janis_mapping 2023-09-27T07:48:48,387 copying janis_core/ingestion/galaxy/janis_mapping/tool.py -> build/lib/janis_core/ingestion/galaxy/janis_mapping 2023-09-27T07:48:48,389 copying janis_core/ingestion/galaxy/janis_mapping/__init__.py -> build/lib/janis_core/ingestion/galaxy/janis_mapping 2023-09-27T07:48:48,391 copying janis_core/ingestion/galaxy/janis_mapping/workflow.py -> build/lib/janis_core/ingestion/galaxy/janis_mapping 2023-09-27T07:48:48,394 creating build/lib/janis_core/ingestion/galaxy/gxtool 2023-09-27T07:48:48,394 copying janis_core/ingestion/galaxy/gxtool/TestRegister.py -> build/lib/janis_core/ingestion/galaxy/gxtool 2023-09-27T07:48:48,396 copying janis_core/ingestion/galaxy/gxtool/mock.py -> build/lib/janis_core/ingestion/galaxy/gxtool 2023-09-27T07:48:48,398 copying janis_core/ingestion/galaxy/gxtool/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool 2023-09-27T07:48:48,400 creating build/lib/janis_core/ingestion/galaxy/internal_model 2023-09-27T07:48:48,401 copying janis_core/ingestion/galaxy/internal_model/__init__.py -> build/lib/janis_core/ingestion/galaxy/internal_model 2023-09-27T07:48:48,403 copying janis_core/ingestion/galaxy/internal_model/protocols.py -> build/lib/janis_core/ingestion/galaxy/internal_model 2023-09-27T07:48:48,405 creating build/lib/janis_core/ingestion/galaxy/runtime 2023-09-27T07:48:48,406 copying janis_core/ingestion/galaxy/runtime/general.py -> build/lib/janis_core/ingestion/galaxy/runtime 2023-09-27T07:48:48,408 copying janis_core/ingestion/galaxy/runtime/tool.py -> build/lib/janis_core/ingestion/galaxy/runtime 2023-09-27T07:48:48,410 copying janis_core/ingestion/galaxy/runtime/dates.py -> build/lib/janis_core/ingestion/galaxy/runtime 2023-09-27T07:48:48,411 copying janis_core/ingestion/galaxy/runtime/exceptions.py -> build/lib/janis_core/ingestion/galaxy/runtime 2023-09-27T07:48:48,413 copying janis_core/ingestion/galaxy/runtime/__init__.py -> build/lib/janis_core/ingestion/galaxy/runtime 2023-09-27T07:48:48,415 creating build/lib/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:48,416 copying janis_core/ingestion/galaxy/containers/Container.py -> build/lib/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:48,418 copying janis_core/ingestion/galaxy/containers/main.py -> build/lib/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:48,419 copying janis_core/ingestion/galaxy/containers/mulled.py -> build/lib/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:48,421 copying janis_core/ingestion/galaxy/containers/__init__.py -> build/lib/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:48,423 copying janis_core/ingestion/galaxy/containers/fetch.py -> build/lib/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:48,424 copying janis_core/ingestion/galaxy/containers/cache.py -> build/lib/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:48,427 creating build/lib/janis_core/ingestion/galaxy/regex_to_glob 2023-09-27T07:48:48,427 copying janis_core/ingestion/galaxy/regex_to_glob/convert.py -> build/lib/janis_core/ingestion/galaxy/regex_to_glob 2023-09-27T07:48:48,429 copying janis_core/ingestion/galaxy/regex_to_glob/patterns.py -> build/lib/janis_core/ingestion/galaxy/regex_to_glob 2023-09-27T07:48:48,431 copying janis_core/ingestion/galaxy/regex_to_glob/common.py -> build/lib/janis_core/ingestion/galaxy/regex_to_glob 2023-09-27T07:48:48,432 copying janis_core/ingestion/galaxy/regex_to_glob/__init__.py -> build/lib/janis_core/ingestion/galaxy/regex_to_glob 2023-09-27T07:48:48,435 creating build/lib/janis_core/ingestion/galaxy/tags 2023-09-27T07:48:48,435 copying janis_core/ingestion/galaxy/tags/groups.py -> build/lib/janis_core/ingestion/galaxy/tags 2023-09-27T07:48:48,437 copying janis_core/ingestion/galaxy/tags/rules.py -> build/lib/janis_core/ingestion/galaxy/tags 2023-09-27T07:48:48,439 copying janis_core/ingestion/galaxy/tags/__init__.py -> build/lib/janis_core/ingestion/galaxy/tags 2023-09-27T07:48:48,441 copying janis_core/ingestion/galaxy/tags/manager.py -> build/lib/janis_core/ingestion/galaxy/tags 2023-09-27T07:48:48,442 copying janis_core/ingestion/galaxy/tags/strategies.py -> build/lib/janis_core/ingestion/galaxy/tags 2023-09-27T07:48:48,444 creating build/lib/janis_core/ingestion/galaxy/utils 2023-09-27T07:48:48,445 copying janis_core/ingestion/galaxy/utils/general.py -> build/lib/janis_core/ingestion/galaxy/utils 2023-09-27T07:48:48,447 copying janis_core/ingestion/galaxy/utils/galaxy.py -> build/lib/janis_core/ingestion/galaxy/utils 2023-09-27T07:48:48,449 copying janis_core/ingestion/galaxy/utils/__init__.py -> build/lib/janis_core/ingestion/galaxy/utils 2023-09-27T07:48:48,450 creating build/lib/janis_core/ingestion/galaxy/fileio 2023-09-27T07:48:48,451 copying janis_core/ingestion/galaxy/fileio/write.py -> build/lib/janis_core/ingestion/galaxy/fileio 2023-09-27T07:48:48,453 copying janis_core/ingestion/galaxy/fileio/initialisation.py -> build/lib/janis_core/ingestion/galaxy/fileio 2023-09-27T07:48:48,455 copying janis_core/ingestion/galaxy/fileio/__init__.py -> build/lib/janis_core/ingestion/galaxy/fileio 2023-09-27T07:48:48,457 creating build/lib/janis_core/ingestion/galaxy/internal_mapping 2023-09-27T07:48:48,458 copying janis_core/ingestion/galaxy/internal_mapping/main.py -> build/lib/janis_core/ingestion/galaxy/internal_mapping 2023-09-27T07:48:48,460 copying janis_core/ingestion/galaxy/internal_mapping/__init__.py -> build/lib/janis_core/ingestion/galaxy/internal_mapping 2023-09-27T07:48:48,462 creating build/lib/janis_core/ingestion/galaxy/expressions 2023-09-27T07:48:48,463 copying janis_core/ingestion/galaxy/expressions/patterns.py -> build/lib/janis_core/ingestion/galaxy/expressions 2023-09-27T07:48:48,465 copying janis_core/ingestion/galaxy/expressions/matches.py -> build/lib/janis_core/ingestion/galaxy/expressions 2023-09-27T07:48:48,466 copying janis_core/ingestion/galaxy/expressions/__init__.py -> build/lib/janis_core/ingestion/galaxy/expressions 2023-09-27T07:48:48,468 copying janis_core/ingestion/galaxy/expressions/checks.py -> build/lib/janis_core/ingestion/galaxy/expressions 2023-09-27T07:48:48,470 creating build/lib/janis_core/ingestion/galaxy/messages 2023-09-27T07:48:48,471 copying janis_core/ingestion/galaxy/messages/messages.py -> build/lib/janis_core/ingestion/galaxy/messages 2023-09-27T07:48:48,473 copying janis_core/ingestion/galaxy/messages/__init__.py -> build/lib/janis_core/ingestion/galaxy/messages 2023-09-27T07:48:48,474 copying janis_core/ingestion/galaxy/messages/logs.py -> build/lib/janis_core/ingestion/galaxy/messages 2023-09-27T07:48:48,476 creating build/lib/janis_core/ingestion/galaxy/gxworkflow/connections 2023-09-27T07:48:48,477 copying janis_core/ingestion/galaxy/gxworkflow/connections/scatter.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/connections 2023-09-27T07:48:48,479 copying janis_core/ingestion/galaxy/gxworkflow/connections/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/connections 2023-09-27T07:48:48,481 creating build/lib/janis_core/ingestion/galaxy/gxworkflow/updates 2023-09-27T07:48:48,482 copying janis_core/ingestion/galaxy/gxworkflow/updates/optionality.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/updates 2023-09-27T07:48:48,484 copying janis_core/ingestion/galaxy/gxworkflow/updates/main.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/updates 2023-09-27T07:48:48,486 copying janis_core/ingestion/galaxy/gxworkflow/updates/arrays.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/updates 2023-09-27T07:48:48,487 copying janis_core/ingestion/galaxy/gxworkflow/updates/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/updates 2023-09-27T07:48:48,489 copying janis_core/ingestion/galaxy/gxworkflow/updates/datatypes.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/updates 2023-09-27T07:48:48,491 creating build/lib/janis_core/ingestion/galaxy/gxworkflow/tool_state 2023-09-27T07:48:48,492 copying janis_core/ingestion/galaxy/gxworkflow/tool_state/filters.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/tool_state 2023-09-27T07:48:48,494 copying janis_core/ingestion/galaxy/gxworkflow/tool_state/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/tool_state 2023-09-27T07:48:48,495 copying janis_core/ingestion/galaxy/gxworkflow/tool_state/load.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/tool_state 2023-09-27T07:48:48,498 creating build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing 2023-09-27T07:48:48,498 copying janis_core/ingestion/galaxy/gxworkflow/parsing/metadata.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing 2023-09-27T07:48:48,500 copying janis_core/ingestion/galaxy/gxworkflow/parsing/step.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing 2023-09-27T07:48:48,502 copying janis_core/ingestion/galaxy/gxworkflow/parsing/inputs.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing 2023-09-27T07:48:48,503 copying janis_core/ingestion/galaxy/gxworkflow/parsing/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing 2023-09-27T07:48:48,505 creating build/lib/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:48,506 copying janis_core/ingestion/galaxy/gxworkflow/values/runtime.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:48,508 copying janis_core/ingestion/galaxy/gxworkflow/values/factory.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:48,510 copying janis_core/ingestion/galaxy/gxworkflow/values/default.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:48,512 copying janis_core/ingestion/galaxy/gxworkflow/values/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:48,513 copying janis_core/ingestion/galaxy/gxworkflow/values/scripts.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:48,515 copying janis_core/ingestion/galaxy/gxworkflow/values/connection.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:48,517 copying janis_core/ingestion/galaxy/gxworkflow/values/static.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:48,519 creating build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step 2023-09-27T07:48:48,520 copying janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/metadata.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step 2023-09-27T07:48:48,522 copying janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/tool.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step 2023-09-27T07:48:48,523 copying janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step 2023-09-27T07:48:48,525 copying janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/outputs.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step 2023-09-27T07:48:48,526 copying janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/prepost.py -> build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step 2023-09-27T07:48:48,528 creating build/lib/janis_core/ingestion/galaxy/gxwrappers/requests 2023-09-27T07:48:48,529 copying janis_core/ingestion/galaxy/gxwrappers/requests/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/requests 2023-09-27T07:48:48,530 copying janis_core/ingestion/galaxy/gxwrappers/requests/versions.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/requests 2023-09-27T07:48:48,533 creating build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:48,534 copying janis_core/ingestion/galaxy/gxwrappers/scraping/wrappers.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:48,536 copying janis_core/ingestion/galaxy/gxwrappers/scraping/scraping.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:48,537 copying janis_core/ingestion/galaxy/gxwrappers/scraping/single.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:48,539 copying janis_core/ingestion/galaxy/gxwrappers/scraping/revisions.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:48,541 copying janis_core/ingestion/galaxy/gxwrappers/scraping/repositories.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:48,543 copying janis_core/ingestion/galaxy/gxwrappers/scraping/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:48,544 copying janis_core/ingestion/galaxy/gxwrappers/scraping/utils.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:48,546 creating build/lib/janis_core/ingestion/galaxy/gxwrappers/wrappers 2023-09-27T07:48:48,547 copying janis_core/ingestion/galaxy/gxwrappers/wrappers/WrapperCache.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/wrappers 2023-09-27T07:48:48,549 copying janis_core/ingestion/galaxy/gxwrappers/wrappers/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/wrappers 2023-09-27T07:48:48,550 copying janis_core/ingestion/galaxy/gxwrappers/wrappers/Wrapper.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/wrappers 2023-09-27T07:48:48,552 creating build/lib/janis_core/ingestion/galaxy/gxwrappers/downloads 2023-09-27T07:48:48,553 copying janis_core/ingestion/galaxy/gxwrappers/downloads/wrappers.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/downloads 2023-09-27T07:48:48,555 copying janis_core/ingestion/galaxy/gxwrappers/downloads/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/downloads 2023-09-27T07:48:48,556 copying janis_core/ingestion/galaxy/gxwrappers/downloads/cache.py -> build/lib/janis_core/ingestion/galaxy/gxwrappers/downloads 2023-09-27T07:48:48,559 creating build/lib/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:48,560 copying janis_core/ingestion/galaxy/gxtool/command/annotation.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:48,563 copying janis_core/ingestion/galaxy/gxtool/command/main.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:48,565 copying janis_core/ingestion/galaxy/gxtool/command/tokenise.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:48,566 copying janis_core/ingestion/galaxy/gxtool/command/epaths.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:48,568 copying janis_core/ingestion/galaxy/gxtool/command/Command.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:48,570 copying janis_core/ingestion/galaxy/gxtool/command/update.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:48,572 copying janis_core/ingestion/galaxy/gxtool/command/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:48,573 copying janis_core/ingestion/galaxy/gxtool/command/loading.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:48,575 creating build/lib/janis_core/ingestion/galaxy/gxtool/text 2023-09-27T07:48:48,576 copying janis_core/ingestion/galaxy/gxtool/text/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/text 2023-09-27T07:48:48,578 copying janis_core/ingestion/galaxy/gxtool/text/utils.py -> build/lib/janis_core/ingestion/galaxy/gxtool/text 2023-09-27T07:48:48,580 creating build/lib/janis_core/ingestion/galaxy/gxtool/parsing 2023-09-27T07:48:48,581 copying janis_core/ingestion/galaxy/gxtool/parsing/main.py -> build/lib/janis_core/ingestion/galaxy/gxtool/parsing 2023-09-27T07:48:48,583 copying janis_core/ingestion/galaxy/gxtool/parsing/param_flattener.py -> build/lib/janis_core/ingestion/galaxy/gxtool/parsing 2023-09-27T07:48:48,585 copying janis_core/ingestion/galaxy/gxtool/parsing/inputs.py -> build/lib/janis_core/ingestion/galaxy/gxtool/parsing 2023-09-27T07:48:48,587 copying janis_core/ingestion/galaxy/gxtool/parsing/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/parsing 2023-09-27T07:48:48,588 copying janis_core/ingestion/galaxy/gxtool/parsing/outputs.py -> build/lib/janis_core/ingestion/galaxy/gxtool/parsing 2023-09-27T07:48:48,591 creating build/lib/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:48,592 copying janis_core/ingestion/galaxy/gxtool/model/citations.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:48,594 copying janis_core/ingestion/galaxy/gxtool/model/requirement.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:48,595 copying janis_core/ingestion/galaxy/gxtool/model/metadata.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:48,597 copying janis_core/ingestion/galaxy/gxtool/model/tool.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:48,599 copying janis_core/ingestion/galaxy/gxtool/model/configfile.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:48,600 copying janis_core/ingestion/galaxy/gxtool/model/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:48,602 copying janis_core/ingestion/galaxy/gxtool/model/tests.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:48,604 copying janis_core/ingestion/galaxy/gxtool/model/script.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:48,606 creating build/lib/janis_core/ingestion/galaxy/gxtool/command/tokens 2023-09-27T07:48:48,607 copying janis_core/ingestion/galaxy/gxtool/command/tokens/factory.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/tokens 2023-09-27T07:48:48,609 copying janis_core/ingestion/galaxy/gxtool/command/tokens/token.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/tokens 2023-09-27T07:48:48,611 copying janis_core/ingestion/galaxy/gxtool/command/tokens/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/tokens 2023-09-27T07:48:48,612 copying janis_core/ingestion/galaxy/gxtool/command/tokens/utils.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/tokens 2023-09-27T07:48:48,614 copying janis_core/ingestion/galaxy/gxtool/command/tokens/prioritisation.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/tokens 2023-09-27T07:48:48,616 creating build/lib/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:48,617 copying janis_core/ingestion/galaxy/gxtool/command/epath/Annotator.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:48,619 copying janis_core/ingestion/galaxy/gxtool/command/epath/analysis.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:48,621 copying janis_core/ingestion/galaxy/gxtool/command/epath/ComponentOrderingStrategy.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:48,623 copying janis_core/ingestion/galaxy/gxtool/command/epath/ExecutionPathAnnotator.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:48,625 copying janis_core/ingestion/galaxy/gxtool/command/epath/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:48,626 copying janis_core/ingestion/galaxy/gxtool/command/epath/ExecutionPath.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:48,628 creating build/lib/janis_core/ingestion/galaxy/gxtool/command/components 2023-09-27T07:48:48,629 copying janis_core/ingestion/galaxy/gxtool/command/components/factory.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components 2023-09-27T07:48:48,631 copying janis_core/ingestion/galaxy/gxtool/command/components/ValueRecord.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components 2023-09-27T07:48:48,633 copying janis_core/ingestion/galaxy/gxtool/command/components/CommandComponent.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components 2023-09-27T07:48:48,635 copying janis_core/ingestion/galaxy/gxtool/command/components/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components 2023-09-27T07:48:48,637 creating build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:48,638 copying janis_core/ingestion/galaxy/gxtool/command/cmdstr/CommandString.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:48,640 copying janis_core/ingestion/galaxy/gxtool/command/cmdstr/MainStatementInferrer.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:48,642 copying janis_core/ingestion/galaxy/gxtool/command/cmdstr/constructs.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:48,644 copying janis_core/ingestion/galaxy/gxtool/command/cmdstr/generate.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:48,646 copying janis_core/ingestion/galaxy/gxtool/command/cmdstr/analysis.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:48,648 copying janis_core/ingestion/galaxy/gxtool/command/cmdstr/RealisedTokenValues.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:48,649 copying janis_core/ingestion/galaxy/gxtool/command/cmdstr/DynamicCommandStatement.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:48,651 copying janis_core/ingestion/galaxy/gxtool/command/cmdstr/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:48,653 copying janis_core/ingestion/galaxy/gxtool/command/cmdstr/utils.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:48,655 creating build/lib/janis_core/ingestion/galaxy/gxtool/command/components/outputs 2023-09-27T07:48:48,656 copying janis_core/ingestion/galaxy/gxtool/command/components/outputs/InputOutput.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/outputs 2023-09-27T07:48:48,659 copying janis_core/ingestion/galaxy/gxtool/command/components/outputs/WildcardOutput.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/outputs 2023-09-27T07:48:48,660 copying janis_core/ingestion/galaxy/gxtool/command/components/outputs/OutputComponent.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/outputs 2023-09-27T07:48:48,663 copying janis_core/ingestion/galaxy/gxtool/command/components/outputs/RedirectOutput.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/outputs 2023-09-27T07:48:48,664 copying janis_core/ingestion/galaxy/gxtool/command/components/outputs/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/outputs 2023-09-27T07:48:48,666 creating build/lib/janis_core/ingestion/galaxy/gxtool/command/components/linux 2023-09-27T07:48:48,667 copying janis_core/ingestion/galaxy/gxtool/command/components/linux/Tee.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/linux 2023-09-27T07:48:48,669 copying janis_core/ingestion/galaxy/gxtool/command/components/linux/streams.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/linux 2023-09-27T07:48:48,670 copying janis_core/ingestion/galaxy/gxtool/command/components/linux/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/linux 2023-09-27T07:48:48,672 creating build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:48,673 copying janis_core/ingestion/galaxy/gxtool/command/components/inputs/Option.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:48,675 copying janis_core/ingestion/galaxy/gxtool/command/components/inputs/InputComponent.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:48,677 copying janis_core/ingestion/galaxy/gxtool/command/components/inputs/Flag.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:48,679 copying janis_core/ingestion/galaxy/gxtool/command/components/inputs/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:48,680 copying janis_core/ingestion/galaxy/gxtool/command/components/inputs/utils.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:48,682 copying janis_core/ingestion/galaxy/gxtool/command/components/inputs/Positional.py -> build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:48,684 creating build/lib/janis_core/ingestion/galaxy/gxtool/text/simplification 2023-09-27T07:48:48,685 copying janis_core/ingestion/galaxy/gxtool/text/simplification/aliases.py -> build/lib/janis_core/ingestion/galaxy/gxtool/text/simplification 2023-09-27T07:48:48,687 copying janis_core/ingestion/galaxy/gxtool/text/simplification/filters.py -> build/lib/janis_core/ingestion/galaxy/gxtool/text/simplification 2023-09-27T07:48:48,689 copying janis_core/ingestion/galaxy/gxtool/text/simplification/simplify.py -> build/lib/janis_core/ingestion/galaxy/gxtool/text/simplification 2023-09-27T07:48:48,691 copying janis_core/ingestion/galaxy/gxtool/text/simplification/main_statement.py -> build/lib/janis_core/ingestion/galaxy/gxtool/text/simplification 2023-09-27T07:48:48,693 copying janis_core/ingestion/galaxy/gxtool/text/simplification/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/text/simplification 2023-09-27T07:48:48,696 creating build/lib/janis_core/ingestion/galaxy/gxtool/text/cheetah 2023-09-27T07:48:48,697 copying janis_core/ingestion/galaxy/gxtool/text/cheetah/evaluation.py -> build/lib/janis_core/ingestion/galaxy/gxtool/text/cheetah 2023-09-27T07:48:48,700 copying janis_core/ingestion/galaxy/gxtool/text/cheetah/blocks.py -> build/lib/janis_core/ingestion/galaxy/gxtool/text/cheetah 2023-09-27T07:48:48,705 copying janis_core/ingestion/galaxy/gxtool/text/cheetah/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/text/cheetah 2023-09-27T07:48:48,709 creating build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:48,712 copying janis_core/ingestion/galaxy/gxtool/parsing/tests/custom_ops.py -> build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:48,718 copying janis_core/ingestion/galaxy/gxtool/parsing/tests/custom_preprocessors.py -> build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:48,724 copying janis_core/ingestion/galaxy/gxtool/parsing/tests/mapper.py -> build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:48,731 copying janis_core/ingestion/galaxy/gxtool/parsing/tests/TestFactoryOld.py -> build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:48,738 copying janis_core/ingestion/galaxy/gxtool/parsing/tests/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:48,743 copying janis_core/ingestion/galaxy/gxtool/parsing/tests/checks.py -> build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:48,751 creating build/lib/janis_core/ingestion/galaxy/gxtool/model/params 2023-09-27T07:48:48,754 copying janis_core/ingestion/galaxy/gxtool/model/params/input_param.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model/params 2023-09-27T07:48:48,762 copying janis_core/ingestion/galaxy/gxtool/model/params/param.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model/params 2023-09-27T07:48:48,768 copying janis_core/ingestion/galaxy/gxtool/model/params/param_register.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model/params 2023-09-27T07:48:48,774 copying janis_core/ingestion/galaxy/gxtool/model/params/output_param.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model/params 2023-09-27T07:48:48,776 copying janis_core/ingestion/galaxy/gxtool/model/params/__init__.py -> build/lib/janis_core/ingestion/galaxy/gxtool/model/params 2023-09-27T07:48:48,778 creating build/lib/janis_core/ingestion/galaxy/internal_model/tool 2023-09-27T07:48:48,779 copying janis_core/ingestion/galaxy/internal_model/tool/tool.py -> build/lib/janis_core/ingestion/galaxy/internal_model/tool 2023-09-27T07:48:48,782 copying janis_core/ingestion/galaxy/internal_model/tool/generate.py -> build/lib/janis_core/ingestion/galaxy/internal_model/tool 2023-09-27T07:48:48,784 copying janis_core/ingestion/galaxy/internal_model/tool/__init__.py -> build/lib/janis_core/ingestion/galaxy/internal_model/tool 2023-09-27T07:48:48,786 copying janis_core/ingestion/galaxy/internal_model/tool/outputs.py -> build/lib/janis_core/ingestion/galaxy/internal_model/tool 2023-09-27T07:48:48,789 creating build/lib/janis_core/ingestion/galaxy/internal_model/workflow 2023-09-27T07:48:48,790 copying janis_core/ingestion/galaxy/internal_model/workflow/metadata.py -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow 2023-09-27T07:48:48,792 copying janis_core/ingestion/galaxy/internal_model/workflow/input.py -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow 2023-09-27T07:48:48,794 copying janis_core/ingestion/galaxy/internal_model/workflow/__init__.py -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow 2023-09-27T07:48:48,796 copying janis_core/ingestion/galaxy/internal_model/workflow/workflow.py -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow 2023-09-27T07:48:48,799 creating build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:48,800 copying janis_core/ingestion/galaxy/internal_model/workflow/step/metadata.py -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:48,802 copying janis_core/ingestion/galaxy/internal_model/workflow/step/step.py -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:48,804 copying janis_core/ingestion/galaxy/internal_model/workflow/step/inputs.py -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:48,807 copying janis_core/ingestion/galaxy/internal_model/workflow/step/__init__.py -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:48,808 copying janis_core/ingestion/galaxy/internal_model/workflow/step/outputs.py -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:48,811 creating build/lib/janis_core/ingestion/galaxy/internal_model/workflow/registers 2023-09-27T07:48:48,812 copying janis_core/ingestion/galaxy/internal_model/workflow/registers/StepOutputRegister.py -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow/registers 2023-09-27T07:48:48,814 copying janis_core/ingestion/galaxy/internal_model/workflow/registers/StepInputRegister.py -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow/registers 2023-09-27T07:48:48,816 copying janis_core/ingestion/galaxy/internal_model/workflow/registers/__init__.py -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow/registers 2023-09-27T07:48:48,818 creating build/lib/janis_core/ingestion/galaxy/runtime/startup 2023-09-27T07:48:48,819 copying janis_core/ingestion/galaxy/runtime/startup/tool.py -> build/lib/janis_core/ingestion/galaxy/runtime/startup 2023-09-27T07:48:48,821 copying janis_core/ingestion/galaxy/runtime/startup/__init__.py -> build/lib/janis_core/ingestion/galaxy/runtime/startup 2023-09-27T07:48:48,823 copying janis_core/ingestion/galaxy/runtime/startup/workflow.py -> build/lib/janis_core/ingestion/galaxy/runtime/startup 2023-09-27T07:48:48,825 creating build/lib/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:48,827 copying janis_core/ingestion/galaxy/containers/fetching/presets.py -> build/lib/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:48,829 copying janis_core/ingestion/galaxy/containers/fetching/GA4GHFetcher.py -> build/lib/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:48,830 copying janis_core/ingestion/galaxy/containers/fetching/ContainerReqFetcher.py -> build/lib/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:48,832 copying janis_core/ingestion/galaxy/containers/fetching/QuayIOFetcher.py -> build/lib/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:48,834 copying janis_core/ingestion/galaxy/containers/fetching/__init__.py -> build/lib/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:48,836 copying janis_core/ingestion/galaxy/containers/fetching/utils.py -> build/lib/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:48,838 copying janis_core/ingestion/galaxy/containers/fetching/Fetcher.py -> build/lib/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:48,841 creating build/lib/janis_core/ingestion/galaxy/containers/selection 2023-09-27T07:48:48,842 copying janis_core/ingestion/galaxy/containers/selection/selection.py -> build/lib/janis_core/ingestion/galaxy/containers/selection 2023-09-27T07:48:48,844 copying janis_core/ingestion/galaxy/containers/selection/VersionMatcher.py -> build/lib/janis_core/ingestion/galaxy/containers/selection 2023-09-27T07:48:48,846 copying janis_core/ingestion/galaxy/containers/selection/__init__.py -> build/lib/janis_core/ingestion/galaxy/containers/selection 2023-09-27T07:48:48,849 creating build/lib/janis_core/ingestion/galaxy/fileio/text 2023-09-27T07:48:48,850 copying janis_core/ingestion/galaxy/fileio/text/TextRender.py -> build/lib/janis_core/ingestion/galaxy/fileio/text 2023-09-27T07:48:48,852 copying janis_core/ingestion/galaxy/fileio/text/formatting.py -> build/lib/janis_core/ingestion/galaxy/fileio/text 2023-09-27T07:48:48,854 copying janis_core/ingestion/galaxy/fileio/text/ordering.py -> build/lib/janis_core/ingestion/galaxy/fileio/text 2023-09-27T07:48:48,857 copying janis_core/ingestion/galaxy/fileio/text/__init__.py -> build/lib/janis_core/ingestion/galaxy/fileio/text 2023-09-27T07:48:48,859 creating build/lib/janis_core/ingestion/galaxy/fileio/formats 2023-09-27T07:48:48,860 copying janis_core/ingestion/galaxy/fileio/formats/DefaultFormat.py -> build/lib/janis_core/ingestion/galaxy/fileio/formats 2023-09-27T07:48:48,862 copying janis_core/ingestion/galaxy/fileio/formats/Format.py -> build/lib/janis_core/ingestion/galaxy/fileio/formats 2023-09-27T07:48:48,864 copying janis_core/ingestion/galaxy/fileio/formats/SubworkflowFormat.py -> build/lib/janis_core/ingestion/galaxy/fileio/formats 2023-09-27T07:48:48,866 copying janis_core/ingestion/galaxy/fileio/formats/__init__.py -> build/lib/janis_core/ingestion/galaxy/fileio/formats 2023-09-27T07:48:48,868 creating build/lib/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:48,869 copying janis_core/ingestion/galaxy/fileio/text/tool/ToolInputSectionText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:48,872 copying janis_core/ingestion/galaxy/fileio/text/tool/UnstranslatedText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:48,874 copying janis_core/ingestion/galaxy/fileio/text/tool/ToolOutputText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:48,877 copying janis_core/ingestion/galaxy/fileio/text/tool/ToolOutputSectionText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:48,879 copying janis_core/ingestion/galaxy/fileio/text/tool/__init__.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:48,880 copying janis_core/ingestion/galaxy/fileio/text/tool/ToolInputText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:48,883 copying janis_core/ingestion/galaxy/fileio/text/tool/ConfigfileText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:48,885 copying janis_core/ingestion/galaxy/fileio/text/tool/ToolText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:48,888 creating build/lib/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:48,889 copying janis_core/ingestion/galaxy/fileio/text/workflow/WorkflowInputText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:48,891 copying janis_core/ingestion/galaxy/fileio/text/workflow/StepText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:48,893 copying janis_core/ingestion/galaxy/fileio/text/workflow/__init__.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:48,895 copying janis_core/ingestion/galaxy/fileio/text/workflow/WorkflowText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:48,898 copying janis_core/ingestion/galaxy/fileio/text/workflow/InputsText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:48,900 copying janis_core/ingestion/galaxy/fileio/text/workflow/ConfigText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:48,902 copying janis_core/ingestion/galaxy/fileio/text/workflow/WorkflowOutputText.py -> build/lib/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:48,905 creating build/lib/janis_core/tests/testtools 2023-09-27T07:48:48,906 copying janis_core/tests/testtools/components.py -> build/lib/janis_core/tests/testtools 2023-09-27T07:48:48,909 copying janis_core/tests/testtools/misc_commandtools.py -> build/lib/janis_core/tests/testtools 2023-09-27T07:48:48,911 copying janis_core/tests/testtools/bwamem.py -> build/lib/janis_core/tests/testtools 2023-09-27T07:48:48,914 copying janis_core/tests/testtools/fastqc.py -> build/lib/janis_core/tests/testtools 2023-09-27T07:48:48,917 copying janis_core/tests/testtools/gridss.py -> build/lib/janis_core/tests/testtools 2023-09-27T07:48:48,919 copying janis_core/tests/testtools/misc_codetools.py -> build/lib/janis_core/tests/testtools 2023-09-27T07:48:48,922 copying janis_core/tests/testtools/unicycler.py -> build/lib/janis_core/tests/testtools 2023-09-27T07:48:48,924 copying janis_core/tests/testtools/types.py -> build/lib/janis_core/tests/testtools 2023-09-27T07:48:48,927 copying janis_core/tests/testtools/basics.py -> build/lib/janis_core/tests/testtools 2023-09-27T07:48:48,929 copying janis_core/tests/testtools/arrays.py -> build/lib/janis_core/tests/testtools 2023-09-27T07:48:48,932 copying janis_core/tests/testtools/__init__.py -> build/lib/janis_core/tests/testtools 2023-09-27T07:48:48,935 creating build/lib/janis_core/tests/mock 2023-09-27T07:48:48,936 copying janis_core/tests/mock/mock_workflow.py -> build/lib/janis_core/tests/mock 2023-09-27T07:48:48,939 copying janis_core/tests/mock/mock_xmltool.py -> build/lib/janis_core/tests/mock 2023-09-27T07:48:48,940 copying janis_core/tests/mock/mock_params.py -> build/lib/janis_core/tests/mock 2023-09-27T07:48:48,943 copying janis_core/tests/mock/mock_entities.py -> build/lib/janis_core/tests/mock 2023-09-27T07:48:48,945 copying janis_core/tests/mock/__init__.py -> build/lib/janis_core/tests/mock 2023-09-27T07:48:48,946 copying janis_core/tests/mock/mock_tool.py -> build/lib/janis_core/tests/mock 2023-09-27T07:48:48,948 copying janis_core/tests/mock/mock_components.py -> build/lib/janis_core/tests/mock 2023-09-27T07:48:48,950 copying janis_core/tests/mock/mock_metadata.py -> build/lib/janis_core/tests/mock 2023-09-27T07:48:48,953 creating build/lib/janis_core/tests/integration 2023-09-27T07:48:48,954 copying janis_core/tests/integration/test_directorygenerator.py -> build/lib/janis_core/tests/integration 2023-09-27T07:48:48,957 copying janis_core/tests/integration/__init__.py -> build/lib/janis_core/tests/integration 2023-09-27T07:48:48,960 creating build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,961 copying janis_core/tests/testworkflows/preprocessing_prune.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,964 copying janis_core/tests/testworkflows/components.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,966 copying janis_core/tests/testworkflows/plumbing_scatter.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,968 copying janis_core/tests/testworkflows/call.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,970 copying janis_core/tests/testworkflows/plumbing_type_mismatch.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,972 copying janis_core/tests/testworkflows/filenames.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,974 copying janis_core/tests/testworkflows/data_sources.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,977 copying janis_core/tests/testworkflows/unwrap.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,979 copying janis_core/tests/testworkflows/minimal_task_inputs.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,981 copying janis_core/tests/testworkflows/all_input_types.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,983 copying janis_core/tests/testworkflows/mandatory_types.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,985 copying janis_core/tests/testworkflows/naming.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,987 copying janis_core/tests/testworkflows/string_formatter.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,989 copying janis_core/tests/testworkflows/basics.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,991 copying janis_core/tests/testworkflows/subworkflow.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,993 copying janis_core/tests/testworkflows/combos.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,994 copying janis_core/tests/testworkflows/scatter.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,996 copying janis_core/tests/testworkflows/assembly.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:48,999 copying janis_core/tests/testworkflows/plumbing_edge_cases.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,000 copying janis_core/tests/testworkflows/trace.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,007 copying janis_core/tests/testworkflows/subworkflow2.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,008 copying janis_core/tests/testworkflows/process_inputs.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,010 copying janis_core/tests/testworkflows/additional_features.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,012 copying janis_core/tests/testworkflows/files_directories_to_create.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,014 copying janis_core/tests/testworkflows/ordering.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,016 copying janis_core/tests/testworkflows/file_pairs.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,018 copying janis_core/tests/testworkflows/__init__.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,020 copying janis_core/tests/testworkflows/optional_types.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,022 copying janis_core/tests/testworkflows/outputs.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,024 copying janis_core/tests/testworkflows/operations.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,026 copying janis_core/tests/testworkflows/duplicate_tasks.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,027 copying janis_core/tests/testworkflows/codetools.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,029 copying janis_core/tests/testworkflows/secondaries.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,031 copying janis_core/tests/testworkflows/script.py -> build/lib/janis_core/tests/testworkflows 2023-09-27T07:48:49,037 creating build/lib/janis_core/tests/mock/cwl 2023-09-27T07:48:49,038 copying janis_core/tests/mock/cwl/workflows.py -> build/lib/janis_core/tests/mock/cwl 2023-09-27T07:48:49,040 copying janis_core/tests/mock/cwl/tools.py -> build/lib/janis_core/tests/mock/cwl 2023-09-27T07:48:49,041 copying janis_core/tests/mock/cwl/__init__.py -> build/lib/janis_core/tests/mock/cwl 2023-09-27T07:48:49,043 creating build/lib/janis_core/settings/ingest 2023-09-27T07:48:49,044 copying janis_core/settings/ingest/cwl.py -> build/lib/janis_core/settings/ingest 2023-09-27T07:48:49,046 copying janis_core/settings/ingest/general.py -> build/lib/janis_core/settings/ingest 2023-09-27T07:48:49,048 copying janis_core/settings/ingest/galaxy.py -> build/lib/janis_core/settings/ingest 2023-09-27T07:48:49,049 copying janis_core/settings/ingest/__init__.py -> build/lib/janis_core/settings/ingest 2023-09-27T07:48:49,052 creating build/lib/janis_core/settings/translate 2023-09-27T07:48:49,052 copying janis_core/settings/translate/general.py -> build/lib/janis_core/settings/translate 2023-09-27T07:48:49,054 copying janis_core/settings/translate/__init__.py -> build/lib/janis_core/settings/translate 2023-09-27T07:48:49,056 copying janis_core/settings/translate/nextflow.py -> build/lib/janis_core/settings/translate 2023-09-27T07:48:49,059 creating build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,059 copying janis_core/redefinitions/tools/vcftools.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,062 copying janis_core/redefinitions/tools/gatk4.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,065 copying janis_core/redefinitions/tools/petermacutils.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,067 copying janis_core/redefinitions/tools/bcftools.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,070 copying janis_core/redefinitions/tools/fastqc.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,072 copying janis_core/redefinitions/tools/gridss.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,074 copying janis_core/redefinitions/tools/echo.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,076 copying janis_core/redefinitions/tools/uncompressarchive.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,078 copying janis_core/redefinitions/tools/bwamem_samtoolsview.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,081 copying janis_core/redefinitions/tools/bioinformaticstool.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,083 copying janis_core/redefinitions/tools/generate.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,085 copying janis_core/redefinitions/tools/performancesummary.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,087 copying janis_core/redefinitions/tools/vardict.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,089 copying janis_core/redefinitions/tools/splitmultiallele.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,091 copying janis_core/redefinitions/tools/manta.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,094 copying janis_core/redefinitions/tools/strelka.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,096 copying janis_core/redefinitions/tools/addbamstats.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,098 copying janis_core/redefinitions/tools/bedtoolsgenomecoverage.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,100 copying janis_core/redefinitions/tools/bgzip.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,102 copying janis_core/redefinitions/tools/parse.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,104 copying janis_core/redefinitions/tools/trimiupac.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,106 copying janis_core/redefinitions/tools/cat.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,108 copying janis_core/redefinitions/tools/cutadapt.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,110 copying janis_core/redefinitions/tools/__init__.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,112 copying janis_core/redefinitions/tools/tabix.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,114 copying janis_core/redefinitions/tools/combinevariants.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,116 copying janis_core/redefinitions/tools/samtools.py -> build/lib/janis_core/redefinitions/tools 2023-09-27T07:48:49,119 creating build/lib/janis_core/redefinitions/workflows 2023-09-27T07:48:49,120 copying janis_core/redefinitions/workflows/wgsgermline.py -> build/lib/janis_core/redefinitions/workflows 2023-09-27T07:48:49,123 copying janis_core/redefinitions/workflows/performancesummarygenome.py -> build/lib/janis_core/redefinitions/workflows 2023-09-27T07:48:49,125 copying janis_core/redefinitions/workflows/bwaaligner.py -> build/lib/janis_core/redefinitions/workflows 2023-09-27T07:48:49,127 copying janis_core/redefinitions/workflows/illuminagermlinevariantcaller.py -> build/lib/janis_core/redefinitions/workflows 2023-09-27T07:48:49,129 copying janis_core/redefinitions/workflows/bioinformaticsworkflow.py -> build/lib/janis_core/redefinitions/workflows 2023-09-27T07:48:49,131 copying janis_core/redefinitions/workflows/addbamstats.py -> build/lib/janis_core/redefinitions/workflows 2023-09-27T07:48:49,133 copying janis_core/redefinitions/workflows/vardictgermlinevariantcaller.py -> build/lib/janis_core/redefinitions/workflows 2023-09-27T07:48:49,134 copying janis_core/redefinitions/workflows/__init__.py -> build/lib/janis_core/redefinitions/workflows 2023-09-27T07:48:49,136 copying janis_core/redefinitions/workflows/gatkgermlinevariantcaller.py -> build/lib/janis_core/redefinitions/workflows 2023-09-27T07:48:49,138 copying janis_core/redefinitions/workflows/mergeandmark.py -> build/lib/janis_core/redefinitions/workflows 2023-09-27T07:48:49,140 copying janis_core/redefinitions/workflows/gatkbaserecalbqsr.py -> build/lib/janis_core/redefinitions/workflows 2023-09-27T07:48:49,142 creating build/lib/janis_core/translations/janis 2023-09-27T07:48:49,143 copying janis_core/translations/janis/main.py -> build/lib/janis_core/translations/janis 2023-09-27T07:48:49,146 copying janis_core/translations/janis/__init__.py -> build/lib/janis_core/translations/janis 2023-09-27T07:48:49,148 creating build/lib/janis_core/translations/cwl 2023-09-27T07:48:49,149 copying janis_core/translations/cwl/main.py -> build/lib/janis_core/translations/cwl 2023-09-27T07:48:49,153 copying janis_core/translations/cwl/__init__.py -> build/lib/janis_core/translations/cwl 2023-09-27T07:48:49,155 creating build/lib/janis_core/translations/common 2023-09-27T07:48:49,156 copying janis_core/translations/common/trace.py -> build/lib/janis_core/translations/common 2023-09-27T07:48:49,158 copying janis_core/translations/common/__init__.py -> build/lib/janis_core/translations/common 2023-09-27T07:48:49,160 creating build/lib/janis_core/translations/nextflow 2023-09-27T07:48:49,161 copying janis_core/translations/nextflow/nulls.py -> build/lib/janis_core/translations/nextflow 2023-09-27T07:48:49,163 copying janis_core/translations/nextflow/variables.py -> build/lib/janis_core/translations/nextflow 2023-09-27T07:48:49,165 copying janis_core/translations/nextflow/expressions.py -> build/lib/janis_core/translations/nextflow 2023-09-27T07:48:49,167 copying janis_core/translations/nextflow/main.py -> build/lib/janis_core/translations/nextflow 2023-09-27T07:48:49,169 copying janis_core/translations/nextflow/scope.py -> build/lib/janis_core/translations/nextflow 2023-09-27T07:48:49,170 copying janis_core/translations/nextflow/unwrap.py -> build/lib/janis_core/translations/nextflow 2023-09-27T07:48:49,173 copying janis_core/translations/nextflow/nfgen_utils.py -> build/lib/janis_core/translations/nextflow 2023-09-27T07:48:49,175 copying janis_core/translations/nextflow/__init__.py -> build/lib/janis_core/translations/nextflow 2023-09-27T07:48:49,177 copying janis_core/translations/nextflow/task_inputs.py -> build/lib/janis_core/translations/nextflow 2023-09-27T07:48:49,179 creating build/lib/janis_core/translations/wdl 2023-09-27T07:48:49,180 copying janis_core/translations/wdl/main.py -> build/lib/janis_core/translations/wdl 2023-09-27T07:48:49,184 copying janis_core/translations/wdl/ordering.py -> build/lib/janis_core/translations/wdl 2023-09-27T07:48:49,186 copying janis_core/translations/wdl/__init__.py -> build/lib/janis_core/translations/wdl 2023-09-27T07:48:49,188 creating build/lib/janis_core/translations/common/preprocessing 2023-09-27T07:48:49,189 copying janis_core/translations/common/preprocessing/__init__.py -> build/lib/janis_core/translations/common/preprocessing 2023-09-27T07:48:49,191 creating build/lib/janis_core/translations/common/preprocessing/builders 2023-09-27T07:48:49,192 copying janis_core/translations/common/preprocessing/builders/main.py -> build/lib/janis_core/translations/common/preprocessing/builders 2023-09-27T07:48:49,194 copying janis_core/translations/common/preprocessing/builders/__init__.py -> build/lib/janis_core/translations/common/preprocessing/builders 2023-09-27T07:48:49,197 creating build/lib/janis_core/translations/common/preprocessing/prune 2023-09-27T07:48:49,198 copying janis_core/translations/common/preprocessing/prune/workflows.py -> build/lib/janis_core/translations/common/preprocessing/prune 2023-09-27T07:48:49,199 copying janis_core/translations/common/preprocessing/prune/main.py -> build/lib/janis_core/translations/common/preprocessing/prune 2023-09-27T07:48:49,201 copying janis_core/translations/common/preprocessing/prune/tools.py -> build/lib/janis_core/translations/common/preprocessing/prune 2023-09-27T07:48:49,203 copying janis_core/translations/common/preprocessing/prune/gather.py -> build/lib/janis_core/translations/common/preprocessing/prune 2023-09-27T07:48:49,205 copying janis_core/translations/common/preprocessing/prune/history.py -> build/lib/janis_core/translations/common/preprocessing/prune 2023-09-27T07:48:49,207 copying janis_core/translations/common/preprocessing/prune/common.py -> build/lib/janis_core/translations/common/preprocessing/prune 2023-09-27T07:48:49,209 copying janis_core/translations/common/preprocessing/prune/__init__.py -> build/lib/janis_core/translations/common/preprocessing/prune 2023-09-27T07:48:49,211 creating build/lib/janis_core/translations/nextflow/generate 2023-09-27T07:48:49,213 copying janis_core/translations/nextflow/generate/config.py -> build/lib/janis_core/translations/nextflow/generate 2023-09-27T07:48:49,215 copying janis_core/translations/nextflow/generate/__init__.py -> build/lib/janis_core/translations/nextflow/generate 2023-09-27T07:48:49,217 creating build/lib/janis_core/translations/nextflow/params 2023-09-27T07:48:49,218 copying janis_core/translations/nextflow/params/main.py -> build/lib/janis_core/translations/nextflow/params 2023-09-27T07:48:49,220 copying janis_core/translations/nextflow/params/update.py -> build/lib/janis_core/translations/nextflow/params 2023-09-27T07:48:49,222 copying janis_core/translations/nextflow/params/__init__.py -> build/lib/janis_core/translations/nextflow/params 2023-09-27T07:48:49,224 creating build/lib/janis_core/translations/nextflow/preprocessing 2023-09-27T07:48:49,225 copying janis_core/translations/nextflow/preprocessing/unique_task_names.py -> build/lib/janis_core/translations/nextflow/preprocessing 2023-09-27T07:48:49,227 copying janis_core/translations/nextflow/preprocessing/__init__.py -> build/lib/janis_core/translations/nextflow/preprocessing 2023-09-27T07:48:49,229 creating build/lib/janis_core/translations/nextflow/naming 2023-09-27T07:48:49,230 copying janis_core/translations/nextflow/naming/constructs.py -> build/lib/janis_core/translations/nextflow/naming 2023-09-27T07:48:49,232 copying janis_core/translations/nextflow/naming/process.py -> build/lib/janis_core/translations/nextflow/naming 2023-09-27T07:48:49,233 copying janis_core/translations/nextflow/naming/__init__.py -> build/lib/janis_core/translations/nextflow/naming 2023-09-27T07:48:49,236 creating build/lib/janis_core/translations/nextflow/casefmt 2023-09-27T07:48:49,237 copying janis_core/translations/nextflow/casefmt/mapping.py -> build/lib/janis_core/translations/nextflow/casefmt 2023-09-27T07:48:49,239 copying janis_core/translations/nextflow/casefmt/patterns.py -> build/lib/janis_core/translations/nextflow/casefmt 2023-09-27T07:48:49,240 copying janis_core/translations/nextflow/casefmt/casefmt.py -> build/lib/janis_core/translations/nextflow/casefmt 2023-09-27T07:48:49,242 copying janis_core/translations/nextflow/casefmt/__init__.py -> build/lib/janis_core/translations/nextflow/casefmt 2023-09-27T07:48:49,244 creating build/lib/janis_core/translations/nextflow/model 2023-09-27T07:48:49,245 copying janis_core/translations/nextflow/model/__init__.py -> build/lib/janis_core/translations/nextflow/model 2023-09-27T07:48:49,247 creating build/lib/janis_core/translations/nextflow/generate/files 2023-09-27T07:48:49,248 copying janis_core/translations/nextflow/generate/files/main.py -> build/lib/janis_core/translations/nextflow/generate/files 2023-09-27T07:48:49,250 copying janis_core/translations/nextflow/generate/files/channel_declarations.py -> build/lib/janis_core/translations/nextflow/generate/files 2023-09-27T07:48:49,253 copying janis_core/translations/nextflow/generate/files/variable_declarations.py -> build/lib/janis_core/translations/nextflow/generate/files 2023-09-27T07:48:49,255 copying janis_core/translations/nextflow/generate/files/process.py -> build/lib/janis_core/translations/nextflow/generate/files 2023-09-27T07:48:49,256 copying janis_core/translations/nextflow/generate/files/__init__.py -> build/lib/janis_core/translations/nextflow/generate/files 2023-09-27T07:48:49,258 copying janis_core/translations/nextflow/generate/files/workflow.py -> build/lib/janis_core/translations/nextflow/generate/files 2023-09-27T07:48:49,261 creating build/lib/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:48:49,262 copying janis_core/translations/nextflow/generate/workflow/call.py -> build/lib/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:48:49,264 copying janis_core/translations/nextflow/generate/workflow/main.py -> build/lib/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:48:49,267 copying janis_core/translations/nextflow/generate/workflow/scatter.py -> build/lib/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:48:49,269 copying janis_core/translations/nextflow/generate/workflow/edge_cases.py -> build/lib/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:48:49,271 copying janis_core/translations/nextflow/generate/workflow/common.py -> build/lib/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:48:49,272 copying janis_core/translations/nextflow/generate/workflow/__init__.py -> build/lib/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:48:49,274 copying janis_core/translations/nextflow/generate/workflow/datatype_mismatch.py -> build/lib/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:48:49,276 creating build/lib/janis_core/translations/nextflow/generate/process 2023-09-27T07:48:49,277 copying janis_core/translations/nextflow/generate/process/main.py -> build/lib/janis_core/translations/nextflow/generate/process 2023-09-27T07:48:49,279 copying janis_core/translations/nextflow/generate/process/inputs.py -> build/lib/janis_core/translations/nextflow/generate/process 2023-09-27T07:48:49,281 copying janis_core/translations/nextflow/generate/process/directives.py -> build/lib/janis_core/translations/nextflow/generate/process 2023-09-27T07:48:49,283 copying janis_core/translations/nextflow/generate/process/__init__.py -> build/lib/janis_core/translations/nextflow/generate/process 2023-09-27T07:48:49,285 creating build/lib/janis_core/translations/nextflow/generate/process/outputs 2023-09-27T07:48:49,286 copying janis_core/translations/nextflow/generate/process/outputs/main.py -> build/lib/janis_core/translations/nextflow/generate/process/outputs 2023-09-27T07:48:49,288 copying janis_core/translations/nextflow/generate/process/outputs/factory_cmdtool.py -> build/lib/janis_core/translations/nextflow/generate/process/outputs 2023-09-27T07:48:49,291 copying janis_core/translations/nextflow/generate/process/outputs/__init__.py -> build/lib/janis_core/translations/nextflow/generate/process/outputs 2023-09-27T07:48:49,292 copying janis_core/translations/nextflow/generate/process/outputs/factory_pythontool.py -> build/lib/janis_core/translations/nextflow/generate/process/outputs 2023-09-27T07:48:49,295 creating build/lib/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:48:49,296 copying janis_core/translations/nextflow/generate/process/script/prescript.py -> build/lib/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:48:49,299 copying janis_core/translations/nextflow/generate/process/script/attributes.py -> build/lib/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:48:49,300 copying janis_core/translations/nextflow/generate/process/script/main.py -> build/lib/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:48:49,303 copying janis_core/translations/nextflow/generate/process/script/selection.py -> build/lib/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:48:49,305 copying janis_core/translations/nextflow/generate/process/script/ctype.py -> build/lib/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:48:49,307 copying janis_core/translations/nextflow/generate/process/script/ordering.py -> build/lib/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:48:49,309 copying janis_core/translations/nextflow/generate/process/script/common.py -> build/lib/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:48:49,311 copying janis_core/translations/nextflow/generate/process/script/__init__.py -> build/lib/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:48:49,313 copying janis_core/translations/nextflow/generate/process/script/script.py -> build/lib/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:48:49,316 creating build/lib/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:48:49,317 copying janis_core/translations/nextflow/preprocessing/task_inputs/main.py -> build/lib/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:48:49,319 copying janis_core/translations/nextflow/preprocessing/task_inputs/history.py -> build/lib/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:48:49,321 copying janis_core/translations/nextflow/preprocessing/task_inputs/common.py -> build/lib/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:48:49,323 copying janis_core/translations/nextflow/preprocessing/task_inputs/__init__.py -> build/lib/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:48:49,324 copying janis_core/translations/nextflow/preprocessing/task_inputs/categories.py -> build/lib/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:48:49,326 copying janis_core/translations/nextflow/preprocessing/task_inputs/populator.py -> build/lib/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:48:49,329 creating build/lib/janis_core/translations/nextflow/model/files 2023-09-27T07:48:49,330 copying janis_core/translations/nextflow/model/files/channels.py -> build/lib/janis_core/translations/nextflow/model/files 2023-09-27T07:48:49,331 copying janis_core/translations/nextflow/model/files/variables.py -> build/lib/janis_core/translations/nextflow/model/files 2023-09-27T07:48:49,333 copying janis_core/translations/nextflow/model/files/files.py -> build/lib/janis_core/translations/nextflow/model/files 2023-09-27T07:48:49,335 copying janis_core/translations/nextflow/model/files/__init__.py -> build/lib/janis_core/translations/nextflow/model/files 2023-09-27T07:48:49,337 creating build/lib/janis_core/translations/nextflow/model/workflow 2023-09-27T07:48:49,338 copying janis_core/translations/nextflow/model/workflow/__init__.py -> build/lib/janis_core/translations/nextflow/model/workflow 2023-09-27T07:48:49,340 copying janis_core/translations/nextflow/model/workflow/workflow.py -> build/lib/janis_core/translations/nextflow/model/workflow 2023-09-27T07:48:49,343 creating build/lib/janis_core/translations/nextflow/model/process 2023-09-27T07:48:49,344 copying janis_core/translations/nextflow/model/process/process.py -> build/lib/janis_core/translations/nextflow/model/process 2023-09-27T07:48:49,346 copying janis_core/translations/nextflow/model/process/inputs.py -> build/lib/janis_core/translations/nextflow/model/process 2023-09-27T07:48:49,348 copying janis_core/translations/nextflow/model/process/directives.py -> build/lib/janis_core/translations/nextflow/model/process 2023-09-27T07:48:49,350 copying janis_core/translations/nextflow/model/process/__init__.py -> build/lib/janis_core/translations/nextflow/model/process 2023-09-27T07:48:49,351 copying janis_core/translations/nextflow/model/process/outputs.py -> build/lib/janis_core/translations/nextflow/model/process 2023-09-27T07:48:49,354 running egg_info 2023-09-27T07:48:49,357 writing janis_pipelines.core.egg-info/PKG-INFO 2023-09-27T07:48:49,362 writing dependency_links to janis_pipelines.core.egg-info/dependency_links.txt 2023-09-27T07:48:49,364 writing requirements to janis_pipelines.core.egg-info/requires.txt 2023-09-27T07:48:49,365 writing top-level names to janis_pipelines.core.egg-info/top_level.txt 2023-09-27T07:48:49,429 reading manifest file 'janis_pipelines.core.egg-info/SOURCES.txt' 2023-09-27T07:48:49,480 adding license file 'LICENSE' 2023-09-27T07:48:49,561 writing manifest file 'janis_pipelines.core.egg-info/SOURCES.txt' 2023-09-27T07:48:49,570 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.ingestion.data' is absent from the `packages` configuration. 2023-09-27T07:48:49,570 !! 2023-09-27T07:48:49,572 ******************************************************************************** 2023-09-27T07:48:49,572 ############################ 2023-09-27T07:48:49,573 # Package would be ignored # 2023-09-27T07:48:49,574 ############################ 2023-09-27T07:48:49,574 Python recognizes 'janis_core.ingestion.data' as an importable package[^1], 2023-09-27T07:48:49,574 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,575 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,575 package, please make sure that 'janis_core.ingestion.data' is explicitly added 2023-09-27T07:48:49,576 to the `packages` configuration field. 2023-09-27T07:48:49,577 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,577 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,578 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,579 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,579 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,580 If you don't want 'janis_core.ingestion.data' to be distributed and are 2023-09-27T07:48:49,581 already explicitly excluding 'janis_core.ingestion.data' via 2023-09-27T07:48:49,581 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,582 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,582 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,583 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,585 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,586 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,587 even if it does not contain any `.py` files. 2023-09-27T07:48:49,587 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,588 directory, all directories are treated like packages. 2023-09-27T07:48:49,589 ******************************************************************************** 2023-09-27T07:48:49,590 !! 2023-09-27T07:48:49,590 check.warn(importable) 2023-09-27T07:48:49,591 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.ingestion.data.galaxy' is absent from the `packages` configuration. 2023-09-27T07:48:49,591 !! 2023-09-27T07:48:49,593 ******************************************************************************** 2023-09-27T07:48:49,593 ############################ 2023-09-27T07:48:49,594 # Package would be ignored # 2023-09-27T07:48:49,594 ############################ 2023-09-27T07:48:49,595 Python recognizes 'janis_core.ingestion.data.galaxy' as an importable package[^1], 2023-09-27T07:48:49,596 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,597 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,597 package, please make sure that 'janis_core.ingestion.data.galaxy' is explicitly added 2023-09-27T07:48:49,598 to the `packages` configuration field. 2023-09-27T07:48:49,599 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,599 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,600 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,601 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,602 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,604 If you don't want 'janis_core.ingestion.data.galaxy' to be distributed and are 2023-09-27T07:48:49,604 already explicitly excluding 'janis_core.ingestion.data.galaxy' via 2023-09-27T07:48:49,605 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,605 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,606 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,606 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,607 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,608 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,609 even if it does not contain any `.py` files. 2023-09-27T07:48:49,609 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,609 directory, all directories are treated like packages. 2023-09-27T07:48:49,610 ******************************************************************************** 2023-09-27T07:48:49,611 !! 2023-09-27T07:48:49,611 check.warn(importable) 2023-09-27T07:48:49,611 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data' is absent from the `packages` configuration. 2023-09-27T07:48:49,612 !! 2023-09-27T07:48:49,613 ******************************************************************************** 2023-09-27T07:48:49,613 ############################ 2023-09-27T07:48:49,613 # Package would be ignored # 2023-09-27T07:48:49,614 ############################ 2023-09-27T07:48:49,615 Python recognizes 'janis_core.tests.data' as an importable package[^1], 2023-09-27T07:48:49,615 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,616 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,617 package, please make sure that 'janis_core.tests.data' is explicitly added 2023-09-27T07:48:49,618 to the `packages` configuration field. 2023-09-27T07:48:49,619 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,619 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,620 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,621 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,622 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,624 If you don't want 'janis_core.tests.data' to be distributed and are 2023-09-27T07:48:49,625 already explicitly excluding 'janis_core.tests.data' via 2023-09-27T07:48:49,625 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,626 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,627 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,628 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,629 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,630 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,631 even if it does not contain any `.py` files. 2023-09-27T07:48:49,631 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,632 directory, all directories are treated like packages. 2023-09-27T07:48:49,633 ******************************************************************************** 2023-09-27T07:48:49,634 !! 2023-09-27T07:48:49,634 check.warn(importable) 2023-09-27T07:48:49,635 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.tools' is absent from the `packages` configuration. 2023-09-27T07:48:49,635 !! 2023-09-27T07:48:49,636 ******************************************************************************** 2023-09-27T07:48:49,636 ############################ 2023-09-27T07:48:49,637 # Package would be ignored # 2023-09-27T07:48:49,637 ############################ 2023-09-27T07:48:49,638 Python recognizes 'janis_core.tests.data.cwl.tools' as an importable package[^1], 2023-09-27T07:48:49,638 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,639 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,639 package, please make sure that 'janis_core.tests.data.cwl.tools' is explicitly added 2023-09-27T07:48:49,640 to the `packages` configuration field. 2023-09-27T07:48:49,640 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,641 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,641 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,642 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,643 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,644 If you don't want 'janis_core.tests.data.cwl.tools' to be distributed and are 2023-09-27T07:48:49,644 already explicitly excluding 'janis_core.tests.data.cwl.tools' via 2023-09-27T07:48:49,645 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,645 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,646 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,646 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,648 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,649 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,650 even if it does not contain any `.py` files. 2023-09-27T07:48:49,651 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,651 directory, all directories are treated like packages. 2023-09-27T07:48:49,652 ******************************************************************************** 2023-09-27T07:48:49,653 !! 2023-09-27T07:48:49,653 check.warn(importable) 2023-09-27T07:48:49,654 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.tools.datatypes' is absent from the `packages` configuration. 2023-09-27T07:48:49,654 !! 2023-09-27T07:48:49,655 ******************************************************************************** 2023-09-27T07:48:49,655 ############################ 2023-09-27T07:48:49,656 # Package would be ignored # 2023-09-27T07:48:49,656 ############################ 2023-09-27T07:48:49,657 Python recognizes 'janis_core.tests.data.cwl.tools.datatypes' as an importable package[^1], 2023-09-27T07:48:49,658 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,659 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,659 package, please make sure that 'janis_core.tests.data.cwl.tools.datatypes' is explicitly added 2023-09-27T07:48:49,660 to the `packages` configuration field. 2023-09-27T07:48:49,661 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,662 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,662 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,663 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,664 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,664 If you don't want 'janis_core.tests.data.cwl.tools.datatypes' to be distributed and are 2023-09-27T07:48:49,665 already explicitly excluding 'janis_core.tests.data.cwl.tools.datatypes' via 2023-09-27T07:48:49,665 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,666 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,666 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,667 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,668 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,669 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,670 even if it does not contain any `.py` files. 2023-09-27T07:48:49,670 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,670 directory, all directories are treated like packages. 2023-09-27T07:48:49,671 ******************************************************************************** 2023-09-27T07:48:49,672 !! 2023-09-27T07:48:49,673 check.warn(importable) 2023-09-27T07:48:49,673 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.tools.expressions' is absent from the `packages` configuration. 2023-09-27T07:48:49,674 !! 2023-09-27T07:48:49,675 ******************************************************************************** 2023-09-27T07:48:49,676 ############################ 2023-09-27T07:48:49,676 # Package would be ignored # 2023-09-27T07:48:49,677 ############################ 2023-09-27T07:48:49,677 Python recognizes 'janis_core.tests.data.cwl.tools.expressions' as an importable package[^1], 2023-09-27T07:48:49,678 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,679 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,680 package, please make sure that 'janis_core.tests.data.cwl.tools.expressions' is explicitly added 2023-09-27T07:48:49,680 to the `packages` configuration field. 2023-09-27T07:48:49,682 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,682 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,683 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,684 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,685 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,686 If you don't want 'janis_core.tests.data.cwl.tools.expressions' to be distributed and are 2023-09-27T07:48:49,687 already explicitly excluding 'janis_core.tests.data.cwl.tools.expressions' via 2023-09-27T07:48:49,687 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,688 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,689 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,690 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,691 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,692 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,693 even if it does not contain any `.py` files. 2023-09-27T07:48:49,693 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,694 directory, all directories are treated like packages. 2023-09-27T07:48:49,694 ******************************************************************************** 2023-09-27T07:48:49,695 !! 2023-09-27T07:48:49,695 check.warn(importable) 2023-09-27T07:48:49,696 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.tools.expressiontools' is absent from the `packages` configuration. 2023-09-27T07:48:49,696 !! 2023-09-27T07:48:49,697 ******************************************************************************** 2023-09-27T07:48:49,697 ############################ 2023-09-27T07:48:49,698 # Package would be ignored # 2023-09-27T07:48:49,698 ############################ 2023-09-27T07:48:49,699 Python recognizes 'janis_core.tests.data.cwl.tools.expressiontools' as an importable package[^1], 2023-09-27T07:48:49,699 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,700 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,700 package, please make sure that 'janis_core.tests.data.cwl.tools.expressiontools' is explicitly added 2023-09-27T07:48:49,701 to the `packages` configuration field. 2023-09-27T07:48:49,702 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,703 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,703 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,705 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,706 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,707 If you don't want 'janis_core.tests.data.cwl.tools.expressiontools' to be distributed and are 2023-09-27T07:48:49,707 already explicitly excluding 'janis_core.tests.data.cwl.tools.expressiontools' via 2023-09-27T07:48:49,708 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,709 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,709 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,710 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,711 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,713 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,714 even if it does not contain any `.py` files. 2023-09-27T07:48:49,714 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,715 directory, all directories are treated like packages. 2023-09-27T07:48:49,715 ******************************************************************************** 2023-09-27T07:48:49,716 !! 2023-09-27T07:48:49,717 check.warn(importable) 2023-09-27T07:48:49,718 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.tools.requirements' is absent from the `packages` configuration. 2023-09-27T07:48:49,718 !! 2023-09-27T07:48:49,719 ******************************************************************************** 2023-09-27T07:48:49,720 ############################ 2023-09-27T07:48:49,720 # Package would be ignored # 2023-09-27T07:48:49,721 ############################ 2023-09-27T07:48:49,721 Python recognizes 'janis_core.tests.data.cwl.tools.requirements' as an importable package[^1], 2023-09-27T07:48:49,722 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,722 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,723 package, please make sure that 'janis_core.tests.data.cwl.tools.requirements' is explicitly added 2023-09-27T07:48:49,723 to the `packages` configuration field. 2023-09-27T07:48:49,724 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,725 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,725 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,726 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,727 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,728 If you don't want 'janis_core.tests.data.cwl.tools.requirements' to be distributed and are 2023-09-27T07:48:49,728 already explicitly excluding 'janis_core.tests.data.cwl.tools.requirements' via 2023-09-27T07:48:49,728 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,729 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,729 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,730 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,732 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,734 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,735 even if it does not contain any `.py` files. 2023-09-27T07:48:49,736 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,736 directory, all directories are treated like packages. 2023-09-27T07:48:49,737 ******************************************************************************** 2023-09-27T07:48:49,738 !! 2023-09-27T07:48:49,739 check.warn(importable) 2023-09-27T07:48:49,739 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.tools.requirements.Python' is absent from the `packages` configuration. 2023-09-27T07:48:49,740 !! 2023-09-27T07:48:49,741 ******************************************************************************** 2023-09-27T07:48:49,742 ############################ 2023-09-27T07:48:49,742 # Package would be ignored # 2023-09-27T07:48:49,744 ############################ 2023-09-27T07:48:49,744 Python recognizes 'janis_core.tests.data.cwl.tools.requirements.Python' as an importable package[^1], 2023-09-27T07:48:49,745 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,784 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,784 package, please make sure that 'janis_core.tests.data.cwl.tools.requirements.Python' is explicitly added 2023-09-27T07:48:49,785 to the `packages` configuration field. 2023-09-27T07:48:49,786 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,786 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,787 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,789 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,789 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,790 If you don't want 'janis_core.tests.data.cwl.tools.requirements.Python' to be distributed and are 2023-09-27T07:48:49,791 already explicitly excluding 'janis_core.tests.data.cwl.tools.requirements.Python' via 2023-09-27T07:48:49,791 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,792 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,792 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,793 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,794 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,795 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,796 even if it does not contain any `.py` files. 2023-09-27T07:48:49,796 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,796 directory, all directories are treated like packages. 2023-09-27T07:48:49,797 ******************************************************************************** 2023-09-27T07:48:49,798 !! 2023-09-27T07:48:49,798 check.warn(importable) 2023-09-27T07:48:49,799 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows' is absent from the `packages` configuration. 2023-09-27T07:48:49,799 !! 2023-09-27T07:48:49,800 ******************************************************************************** 2023-09-27T07:48:49,801 ############################ 2023-09-27T07:48:49,801 # Package would be ignored # 2023-09-27T07:48:49,802 ############################ 2023-09-27T07:48:49,802 Python recognizes 'janis_core.tests.data.cwl.workflows' as an importable package[^1], 2023-09-27T07:48:49,803 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,804 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,805 package, please make sure that 'janis_core.tests.data.cwl.workflows' is explicitly added 2023-09-27T07:48:49,805 to the `packages` configuration field. 2023-09-27T07:48:49,806 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,807 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,808 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,808 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,809 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,810 If you don't want 'janis_core.tests.data.cwl.workflows' to be distributed and are 2023-09-27T07:48:49,811 already explicitly excluding 'janis_core.tests.data.cwl.workflows' via 2023-09-27T07:48:49,811 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,812 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,812 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,813 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,815 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,816 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,817 even if it does not contain any `.py` files. 2023-09-27T07:48:49,818 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,818 directory, all directories are treated like packages. 2023-09-27T07:48:49,819 ******************************************************************************** 2023-09-27T07:48:49,819 !! 2023-09-27T07:48:49,820 check.warn(importable) 2023-09-27T07:48:49,820 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.CroMaSt' is absent from the `packages` configuration. 2023-09-27T07:48:49,820 !! 2023-09-27T07:48:49,821 ******************************************************************************** 2023-09-27T07:48:49,821 ############################ 2023-09-27T07:48:49,822 # Package would be ignored # 2023-09-27T07:48:49,822 ############################ 2023-09-27T07:48:49,823 Python recognizes 'janis_core.tests.data.cwl.workflows.CroMaSt' as an importable package[^1], 2023-09-27T07:48:49,823 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,824 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,824 package, please make sure that 'janis_core.tests.data.cwl.workflows.CroMaSt' is explicitly added 2023-09-27T07:48:49,824 to the `packages` configuration field. 2023-09-27T07:48:49,825 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,826 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,826 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,827 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,828 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,829 If you don't want 'janis_core.tests.data.cwl.workflows.CroMaSt' to be distributed and are 2023-09-27T07:48:49,829 already explicitly excluding 'janis_core.tests.data.cwl.workflows.CroMaSt' via 2023-09-27T07:48:49,830 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,830 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,831 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,832 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,833 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,834 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,835 even if it does not contain any `.py` files. 2023-09-27T07:48:49,835 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,836 directory, all directories are treated like packages. 2023-09-27T07:48:49,836 ******************************************************************************** 2023-09-27T07:48:49,837 !! 2023-09-27T07:48:49,838 check.warn(importable) 2023-09-27T07:48:49,838 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.CroMaSt.Tools' is absent from the `packages` configuration. 2023-09-27T07:48:49,839 !! 2023-09-27T07:48:49,840 ******************************************************************************** 2023-09-27T07:48:49,840 ############################ 2023-09-27T07:48:49,841 # Package would be ignored # 2023-09-27T07:48:49,841 ############################ 2023-09-27T07:48:49,842 Python recognizes 'janis_core.tests.data.cwl.workflows.CroMaSt.Tools' as an importable package[^1], 2023-09-27T07:48:49,842 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,844 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,844 package, please make sure that 'janis_core.tests.data.cwl.workflows.CroMaSt.Tools' is explicitly added 2023-09-27T07:48:49,844 to the `packages` configuration field. 2023-09-27T07:48:49,845 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,845 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,846 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,846 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,847 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,848 If you don't want 'janis_core.tests.data.cwl.workflows.CroMaSt.Tools' to be distributed and are 2023-09-27T07:48:49,848 already explicitly excluding 'janis_core.tests.data.cwl.workflows.CroMaSt.Tools' via 2023-09-27T07:48:49,848 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,849 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,849 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,850 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,851 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,852 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,852 even if it does not contain any `.py` files. 2023-09-27T07:48:49,853 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,853 directory, all directories are treated like packages. 2023-09-27T07:48:49,854 ******************************************************************************** 2023-09-27T07:48:49,855 !! 2023-09-27T07:48:49,855 check.warn(importable) 2023-09-27T07:48:49,856 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.CroMaSt.Tools.Python' is absent from the `packages` configuration. 2023-09-27T07:48:49,856 !! 2023-09-27T07:48:49,857 ******************************************************************************** 2023-09-27T07:48:49,858 ############################ 2023-09-27T07:48:49,858 # Package would be ignored # 2023-09-27T07:48:49,859 ############################ 2023-09-27T07:48:49,859 Python recognizes 'janis_core.tests.data.cwl.workflows.CroMaSt.Tools.Python' as an importable package[^1], 2023-09-27T07:48:49,861 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,862 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,862 package, please make sure that 'janis_core.tests.data.cwl.workflows.CroMaSt.Tools.Python' is explicitly added 2023-09-27T07:48:49,863 to the `packages` configuration field. 2023-09-27T07:48:49,864 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,864 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,865 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,866 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,867 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,868 If you don't want 'janis_core.tests.data.cwl.workflows.CroMaSt.Tools.Python' to be distributed and are 2023-09-27T07:48:49,869 already explicitly excluding 'janis_core.tests.data.cwl.workflows.CroMaSt.Tools.Python' via 2023-09-27T07:48:49,869 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,870 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,870 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,871 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,872 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,873 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,873 even if it does not contain any `.py` files. 2023-09-27T07:48:49,874 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,874 directory, all directories are treated like packages. 2023-09-27T07:48:49,874 ******************************************************************************** 2023-09-27T07:48:49,875 !! 2023-09-27T07:48:49,875 check.warn(importable) 2023-09-27T07:48:49,876 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.CroMaSt.translated' is absent from the `packages` configuration. 2023-09-27T07:48:49,876 !! 2023-09-27T07:48:49,877 ******************************************************************************** 2023-09-27T07:48:49,877 ############################ 2023-09-27T07:48:49,878 # Package would be ignored # 2023-09-27T07:48:49,878 ############################ 2023-09-27T07:48:49,879 Python recognizes 'janis_core.tests.data.cwl.workflows.CroMaSt.translated' as an importable package[^1], 2023-09-27T07:48:49,879 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,880 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,881 package, please make sure that 'janis_core.tests.data.cwl.workflows.CroMaSt.translated' is explicitly added 2023-09-27T07:48:49,881 to the `packages` configuration field. 2023-09-27T07:48:49,883 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,883 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,884 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,885 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,886 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,887 If you don't want 'janis_core.tests.data.cwl.workflows.CroMaSt.translated' to be distributed and are 2023-09-27T07:48:49,887 already explicitly excluding 'janis_core.tests.data.cwl.workflows.CroMaSt.translated' via 2023-09-27T07:48:49,888 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,888 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,889 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,889 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,891 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,892 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,893 even if it does not contain any `.py` files. 2023-09-27T07:48:49,893 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,894 directory, all directories are treated like packages. 2023-09-27T07:48:49,894 ******************************************************************************** 2023-09-27T07:48:49,896 !! 2023-09-27T07:48:49,896 check.warn(importable) 2023-09-27T07:48:49,896 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.CroMaSt.yml' is absent from the `packages` configuration. 2023-09-27T07:48:49,897 !! 2023-09-27T07:48:49,898 ******************************************************************************** 2023-09-27T07:48:49,898 ############################ 2023-09-27T07:48:49,898 # Package would be ignored # 2023-09-27T07:48:49,899 ############################ 2023-09-27T07:48:49,899 Python recognizes 'janis_core.tests.data.cwl.workflows.CroMaSt.yml' as an importable package[^1], 2023-09-27T07:48:49,899 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,900 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,901 package, please make sure that 'janis_core.tests.data.cwl.workflows.CroMaSt.yml' is explicitly added 2023-09-27T07:48:49,901 to the `packages` configuration field. 2023-09-27T07:48:49,902 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,903 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,903 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,904 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,905 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,906 If you don't want 'janis_core.tests.data.cwl.workflows.CroMaSt.yml' to be distributed and are 2023-09-27T07:48:49,906 already explicitly excluding 'janis_core.tests.data.cwl.workflows.CroMaSt.yml' via 2023-09-27T07:48:49,907 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,907 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,908 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,909 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,910 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,912 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,912 even if it does not contain any `.py` files. 2023-09-27T07:48:49,913 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,913 directory, all directories are treated like packages. 2023-09-27T07:48:49,914 ******************************************************************************** 2023-09-27T07:48:49,915 !! 2023-09-27T07:48:49,916 check.warn(importable) 2023-09-27T07:48:49,916 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.align_sort_markdup' is absent from the `packages` configuration. 2023-09-27T07:48:49,917 !! 2023-09-27T07:48:49,918 ******************************************************************************** 2023-09-27T07:48:49,919 ############################ 2023-09-27T07:48:49,920 # Package would be ignored # 2023-09-27T07:48:49,921 ############################ 2023-09-27T07:48:49,922 Python recognizes 'janis_core.tests.data.cwl.workflows.align_sort_markdup' as an importable package[^1], 2023-09-27T07:48:49,923 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,926 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,928 package, please make sure that 'janis_core.tests.data.cwl.workflows.align_sort_markdup' is explicitly added 2023-09-27T07:48:49,930 to the `packages` configuration field. 2023-09-27T07:48:49,935 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,938 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,940 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,941 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,942 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,942 If you don't want 'janis_core.tests.data.cwl.workflows.align_sort_markdup' to be distributed and are 2023-09-27T07:48:49,943 already explicitly excluding 'janis_core.tests.data.cwl.workflows.align_sort_markdup' via 2023-09-27T07:48:49,943 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,943 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,944 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,944 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,945 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,946 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,947 even if it does not contain any `.py` files. 2023-09-27T07:48:49,949 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,949 directory, all directories are treated like packages. 2023-09-27T07:48:49,950 ******************************************************************************** 2023-09-27T07:48:49,951 !! 2023-09-27T07:48:49,952 check.warn(importable) 2023-09-27T07:48:49,952 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.align_sort_markdup.subworkflows' is absent from the `packages` configuration. 2023-09-27T07:48:49,953 !! 2023-09-27T07:48:49,953 ******************************************************************************** 2023-09-27T07:48:49,954 ############################ 2023-09-27T07:48:49,954 # Package would be ignored # 2023-09-27T07:48:49,955 ############################ 2023-09-27T07:48:49,956 Python recognizes 'janis_core.tests.data.cwl.workflows.align_sort_markdup.subworkflows' as an importable package[^1], 2023-09-27T07:48:49,956 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,957 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,957 package, please make sure that 'janis_core.tests.data.cwl.workflows.align_sort_markdup.subworkflows' is explicitly added 2023-09-27T07:48:49,958 to the `packages` configuration field. 2023-09-27T07:48:49,959 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,959 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,960 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,961 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,962 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,963 If you don't want 'janis_core.tests.data.cwl.workflows.align_sort_markdup.subworkflows' to be distributed and are 2023-09-27T07:48:49,964 already explicitly excluding 'janis_core.tests.data.cwl.workflows.align_sort_markdup.subworkflows' via 2023-09-27T07:48:49,964 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,965 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,965 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,966 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,967 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,968 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,968 even if it does not contain any `.py` files. 2023-09-27T07:48:49,968 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,969 directory, all directories are treated like packages. 2023-09-27T07:48:49,969 ******************************************************************************** 2023-09-27T07:48:49,970 !! 2023-09-27T07:48:49,970 check.warn(importable) 2023-09-27T07:48:49,971 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.align_sort_markdup.tools' is absent from the `packages` configuration. 2023-09-27T07:48:49,971 !! 2023-09-27T07:48:49,972 ******************************************************************************** 2023-09-27T07:48:49,973 ############################ 2023-09-27T07:48:49,973 # Package would be ignored # 2023-09-27T07:48:49,974 ############################ 2023-09-27T07:48:49,974 Python recognizes 'janis_core.tests.data.cwl.workflows.align_sort_markdup.tools' as an importable package[^1], 2023-09-27T07:48:49,975 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,976 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,976 package, please make sure that 'janis_core.tests.data.cwl.workflows.align_sort_markdup.tools' is explicitly added 2023-09-27T07:48:49,977 to the `packages` configuration field. 2023-09-27T07:48:49,978 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,978 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,979 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,980 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,981 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,982 If you don't want 'janis_core.tests.data.cwl.workflows.align_sort_markdup.tools' to be distributed and are 2023-09-27T07:48:49,982 already explicitly excluding 'janis_core.tests.data.cwl.workflows.align_sort_markdup.tools' via 2023-09-27T07:48:49,983 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:49,983 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:49,984 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:49,985 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:49,985 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:49,987 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:49,988 even if it does not contain any `.py` files. 2023-09-27T07:48:49,988 On the other hand, currently there is no concept of package data 2023-09-27T07:48:49,989 directory, all directories are treated like packages. 2023-09-27T07:48:49,989 ******************************************************************************** 2023-09-27T07:48:49,990 !! 2023-09-27T07:48:49,991 check.warn(importable) 2023-09-27T07:48:49,991 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.structuralvariants' is absent from the `packages` configuration. 2023-09-27T07:48:49,991 !! 2023-09-27T07:48:49,992 ******************************************************************************** 2023-09-27T07:48:49,992 ############################ 2023-09-27T07:48:49,993 # Package would be ignored # 2023-09-27T07:48:49,993 ############################ 2023-09-27T07:48:49,994 Python recognizes 'janis_core.tests.data.cwl.workflows.structuralvariants' as an importable package[^1], 2023-09-27T07:48:49,994 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:49,995 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:49,995 package, please make sure that 'janis_core.tests.data.cwl.workflows.structuralvariants' is explicitly added 2023-09-27T07:48:49,995 to the `packages` configuration field. 2023-09-27T07:48:49,996 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:49,996 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:49,997 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:49,997 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:49,998 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:49,999 If you don't want 'janis_core.tests.data.cwl.workflows.structuralvariants' to be distributed and are 2023-09-27T07:48:50,000 already explicitly excluding 'janis_core.tests.data.cwl.workflows.structuralvariants' via 2023-09-27T07:48:50,000 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,001 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,001 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,002 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,003 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,005 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,005 even if it does not contain any `.py` files. 2023-09-27T07:48:50,006 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,006 directory, all directories are treated like packages. 2023-09-27T07:48:50,007 ******************************************************************************** 2023-09-27T07:48:50,008 !! 2023-09-27T07:48:50,008 check.warn(importable) 2023-09-27T07:48:50,009 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_operations' is absent from the `packages` configuration. 2023-09-27T07:48:50,009 !! 2023-09-27T07:48:50,010 ******************************************************************************** 2023-09-27T07:48:50,011 ############################ 2023-09-27T07:48:50,011 # Package would be ignored # 2023-09-27T07:48:50,012 ############################ 2023-09-27T07:48:50,012 Python recognizes 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_operations' as an importable package[^1], 2023-09-27T07:48:50,013 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,015 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,015 package, please make sure that 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_operations' is explicitly added 2023-09-27T07:48:50,016 to the `packages` configuration field. 2023-09-27T07:48:50,016 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,017 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,023 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,024 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,024 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,025 If you don't want 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_operations' to be distributed and are 2023-09-27T07:48:50,026 already explicitly excluding 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_operations' via 2023-09-27T07:48:50,026 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,027 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,027 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,028 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,029 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,030 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,030 even if it does not contain any `.py` files. 2023-09-27T07:48:50,031 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,032 directory, all directories are treated like packages. 2023-09-27T07:48:50,032 ******************************************************************************** 2023-09-27T07:48:50,033 !! 2023-09-27T07:48:50,034 check.warn(importable) 2023-09-27T07:48:50,035 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_operations.subworkflows' is absent from the `packages` configuration. 2023-09-27T07:48:50,035 !! 2023-09-27T07:48:50,036 ******************************************************************************** 2023-09-27T07:48:50,037 ############################ 2023-09-27T07:48:50,037 # Package would be ignored # 2023-09-27T07:48:50,038 ############################ 2023-09-27T07:48:50,038 Python recognizes 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_operations.subworkflows' as an importable package[^1], 2023-09-27T07:48:50,039 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,040 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,040 package, please make sure that 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_operations.subworkflows' is explicitly added 2023-09-27T07:48:50,041 to the `packages` configuration field. 2023-09-27T07:48:50,042 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,042 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,043 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,044 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,045 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,046 If you don't want 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_operations.subworkflows' to be distributed and are 2023-09-27T07:48:50,047 already explicitly excluding 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_operations.subworkflows' via 2023-09-27T07:48:50,048 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,048 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,048 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,049 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,050 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,051 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,051 even if it does not contain any `.py` files. 2023-09-27T07:48:50,052 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,052 directory, all directories are treated like packages. 2023-09-27T07:48:50,053 ******************************************************************************** 2023-09-27T07:48:50,054 !! 2023-09-27T07:48:50,054 check.warn(importable) 2023-09-27T07:48:50,055 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_workflow' is absent from the `packages` configuration. 2023-09-27T07:48:50,055 !! 2023-09-27T07:48:50,056 ******************************************************************************** 2023-09-27T07:48:50,057 ############################ 2023-09-27T07:48:50,057 # Package would be ignored # 2023-09-27T07:48:50,058 ############################ 2023-09-27T07:48:50,058 Python recognizes 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_workflow' as an importable package[^1], 2023-09-27T07:48:50,059 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,060 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,061 package, please make sure that 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_workflow' is explicitly added 2023-09-27T07:48:50,061 to the `packages` configuration field. 2023-09-27T07:48:50,062 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,063 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,063 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,064 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,065 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,066 If you don't want 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_workflow' to be distributed and are 2023-09-27T07:48:50,066 already explicitly excluding 'janis_core.tests.data.cwl.workflows.structuralvariants.abstract_workflow' via 2023-09-27T07:48:50,067 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,067 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,068 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,069 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,070 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,071 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,072 even if it does not contain any `.py` files. 2023-09-27T07:48:50,072 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,073 directory, all directories are treated like packages. 2023-09-27T07:48:50,074 ******************************************************************************** 2023-09-27T07:48:50,074 !! 2023-09-27T07:48:50,075 check.warn(importable) 2023-09-27T07:48:50,075 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.structuralvariants.subworkflows' is absent from the `packages` configuration. 2023-09-27T07:48:50,075 !! 2023-09-27T07:48:50,076 ******************************************************************************** 2023-09-27T07:48:50,076 ############################ 2023-09-27T07:48:50,077 # Package would be ignored # 2023-09-27T07:48:50,077 ############################ 2023-09-27T07:48:50,078 Python recognizes 'janis_core.tests.data.cwl.workflows.structuralvariants.subworkflows' as an importable package[^1], 2023-09-27T07:48:50,078 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,079 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,079 package, please make sure that 'janis_core.tests.data.cwl.workflows.structuralvariants.subworkflows' is explicitly added 2023-09-27T07:48:50,079 to the `packages` configuration field. 2023-09-27T07:48:50,080 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,081 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,081 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,082 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,083 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,085 If you don't want 'janis_core.tests.data.cwl.workflows.structuralvariants.subworkflows' to be distributed and are 2023-09-27T07:48:50,085 already explicitly excluding 'janis_core.tests.data.cwl.workflows.structuralvariants.subworkflows' via 2023-09-27T07:48:50,086 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,086 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,087 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,088 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,089 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,090 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,091 even if it does not contain any `.py` files. 2023-09-27T07:48:50,091 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,092 directory, all directories are treated like packages. 2023-09-27T07:48:50,092 ******************************************************************************** 2023-09-27T07:48:50,094 !! 2023-09-27T07:48:50,094 check.warn(importable) 2023-09-27T07:48:50,095 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.structuralvariants.tools' is absent from the `packages` configuration. 2023-09-27T07:48:50,095 !! 2023-09-27T07:48:50,096 ******************************************************************************** 2023-09-27T07:48:50,097 ############################ 2023-09-27T07:48:50,097 # Package would be ignored # 2023-09-27T07:48:50,098 ############################ 2023-09-27T07:48:50,099 Python recognizes 'janis_core.tests.data.cwl.workflows.structuralvariants.tools' as an importable package[^1], 2023-09-27T07:48:50,100 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,101 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,101 package, please make sure that 'janis_core.tests.data.cwl.workflows.structuralvariants.tools' is explicitly added 2023-09-27T07:48:50,101 to the `packages` configuration field. 2023-09-27T07:48:50,102 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,103 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,103 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,104 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,104 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,105 If you don't want 'janis_core.tests.data.cwl.workflows.structuralvariants.tools' to be distributed and are 2023-09-27T07:48:50,106 already explicitly excluding 'janis_core.tests.data.cwl.workflows.structuralvariants.tools' via 2023-09-27T07:48:50,106 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,107 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,107 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,108 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,109 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,110 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,110 even if it does not contain any `.py` files. 2023-09-27T07:48:50,111 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,111 directory, all directories are treated like packages. 2023-09-27T07:48:50,112 ******************************************************************************** 2023-09-27T07:48:50,113 !! 2023-09-27T07:48:50,113 check.warn(importable) 2023-09-27T07:48:50,114 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.cwl.workflows.subworkflow_test' is absent from the `packages` configuration. 2023-09-27T07:48:50,114 !! 2023-09-27T07:48:50,115 ******************************************************************************** 2023-09-27T07:48:50,116 ############################ 2023-09-27T07:48:50,116 # Package would be ignored # 2023-09-27T07:48:50,117 ############################ 2023-09-27T07:48:50,117 Python recognizes 'janis_core.tests.data.cwl.workflows.subworkflow_test' as an importable package[^1], 2023-09-27T07:48:50,117 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,119 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,119 package, please make sure that 'janis_core.tests.data.cwl.workflows.subworkflow_test' is explicitly added 2023-09-27T07:48:50,119 to the `packages` configuration field. 2023-09-27T07:48:50,121 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,121 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,122 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,123 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,124 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,125 If you don't want 'janis_core.tests.data.cwl.workflows.subworkflow_test' to be distributed and are 2023-09-27T07:48:50,126 already explicitly excluding 'janis_core.tests.data.cwl.workflows.subworkflow_test' via 2023-09-27T07:48:50,126 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,126 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,127 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,128 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,128 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,130 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,130 even if it does not contain any `.py` files. 2023-09-27T07:48:50,130 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,131 directory, all directories are treated like packages. 2023-09-27T07:48:50,131 ******************************************************************************** 2023-09-27T07:48:50,132 !! 2023-09-27T07:48:50,132 check.warn(importable) 2023-09-27T07:48:50,133 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.galaxy' is absent from the `packages` configuration. 2023-09-27T07:48:50,133 !! 2023-09-27T07:48:50,134 ******************************************************************************** 2023-09-27T07:48:50,135 ############################ 2023-09-27T07:48:50,135 # Package would be ignored # 2023-09-27T07:48:50,136 ############################ 2023-09-27T07:48:50,136 Python recognizes 'janis_core.tests.data.galaxy' as an importable package[^1], 2023-09-27T07:48:50,137 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,138 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,138 package, please make sure that 'janis_core.tests.data.galaxy' is explicitly added 2023-09-27T07:48:50,139 to the `packages` configuration field. 2023-09-27T07:48:50,140 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,140 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,141 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,142 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,143 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,144 If you don't want 'janis_core.tests.data.galaxy' to be distributed and are 2023-09-27T07:48:50,145 already explicitly excluding 'janis_core.tests.data.galaxy' via 2023-09-27T07:48:50,145 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,145 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,146 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,147 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,148 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,150 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,150 even if it does not contain any `.py` files. 2023-09-27T07:48:50,151 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,151 directory, all directories are treated like packages. 2023-09-27T07:48:50,152 ******************************************************************************** 2023-09-27T07:48:50,153 !! 2023-09-27T07:48:50,153 check.warn(importable) 2023-09-27T07:48:50,154 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.galaxy.abricate' is absent from the `packages` configuration. 2023-09-27T07:48:50,154 !! 2023-09-27T07:48:50,155 ******************************************************************************** 2023-09-27T07:48:50,155 ############################ 2023-09-27T07:48:50,156 # Package would be ignored # 2023-09-27T07:48:50,156 ############################ 2023-09-27T07:48:50,156 Python recognizes 'janis_core.tests.data.galaxy.abricate' as an importable package[^1], 2023-09-27T07:48:50,157 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,158 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,158 package, please make sure that 'janis_core.tests.data.galaxy.abricate' is explicitly added 2023-09-27T07:48:50,158 to the `packages` configuration field. 2023-09-27T07:48:50,159 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,160 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,160 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,161 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,162 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,163 If you don't want 'janis_core.tests.data.galaxy.abricate' to be distributed and are 2023-09-27T07:48:50,164 already explicitly excluding 'janis_core.tests.data.galaxy.abricate' via 2023-09-27T07:48:50,164 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,165 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,165 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,166 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,167 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,169 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,170 even if it does not contain any `.py` files. 2023-09-27T07:48:50,170 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,171 directory, all directories are treated like packages. 2023-09-27T07:48:50,171 ******************************************************************************** 2023-09-27T07:48:50,172 !! 2023-09-27T07:48:50,173 check.warn(importable) 2023-09-27T07:48:50,173 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.janis' is absent from the `packages` configuration. 2023-09-27T07:48:50,174 !! 2023-09-27T07:48:50,175 ******************************************************************************** 2023-09-27T07:48:50,175 ############################ 2023-09-27T07:48:50,175 # Package would be ignored # 2023-09-27T07:48:50,176 ############################ 2023-09-27T07:48:50,177 Python recognizes 'janis_core.tests.data.janis' as an importable package[^1], 2023-09-27T07:48:50,177 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,178 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,179 package, please make sure that 'janis_core.tests.data.janis' is explicitly added 2023-09-27T07:48:50,179 to the `packages` configuration field. 2023-09-27T07:48:50,181 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,181 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,181 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,182 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,183 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,184 If you don't want 'janis_core.tests.data.janis' to be distributed and are 2023-09-27T07:48:50,184 already explicitly excluding 'janis_core.tests.data.janis' via 2023-09-27T07:48:50,185 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,185 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,185 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,186 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,187 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,188 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,189 even if it does not contain any `.py` files. 2023-09-27T07:48:50,189 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,190 directory, all directories are treated like packages. 2023-09-27T07:48:50,190 ******************************************************************************** 2023-09-27T07:48:50,191 !! 2023-09-27T07:48:50,192 check.warn(importable) 2023-09-27T07:48:50,192 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.janis.simple' is absent from the `packages` configuration. 2023-09-27T07:48:50,193 !! 2023-09-27T07:48:50,194 ******************************************************************************** 2023-09-27T07:48:50,194 ############################ 2023-09-27T07:48:50,195 # Package would be ignored # 2023-09-27T07:48:50,195 ############################ 2023-09-27T07:48:50,196 Python recognizes 'janis_core.tests.data.janis.simple' as an importable package[^1], 2023-09-27T07:48:50,196 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,197 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,198 package, please make sure that 'janis_core.tests.data.janis.simple' is explicitly added 2023-09-27T07:48:50,198 to the `packages` configuration field. 2023-09-27T07:48:50,199 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,200 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,200 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,201 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,202 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,204 If you don't want 'janis_core.tests.data.janis.simple' to be distributed and are 2023-09-27T07:48:50,204 already explicitly excluding 'janis_core.tests.data.janis.simple' via 2023-09-27T07:48:50,205 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,205 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,206 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,207 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,208 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,209 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,210 even if it does not contain any `.py` files. 2023-09-27T07:48:50,211 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,212 directory, all directories are treated like packages. 2023-09-27T07:48:50,212 ******************************************************************************** 2023-09-27T07:48:50,213 !! 2023-09-27T07:48:50,213 check.warn(importable) 2023-09-27T07:48:50,214 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.janis.simple.scripts' is absent from the `packages` configuration. 2023-09-27T07:48:50,214 !! 2023-09-27T07:48:50,215 ******************************************************************************** 2023-09-27T07:48:50,215 ############################ 2023-09-27T07:48:50,216 # Package would be ignored # 2023-09-27T07:48:50,216 ############################ 2023-09-27T07:48:50,217 Python recognizes 'janis_core.tests.data.janis.simple.scripts' as an importable package[^1], 2023-09-27T07:48:50,217 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,219 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,220 package, please make sure that 'janis_core.tests.data.janis.simple.scripts' is explicitly added 2023-09-27T07:48:50,220 to the `packages` configuration field. 2023-09-27T07:48:50,221 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,221 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,222 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,223 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,224 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,225 If you don't want 'janis_core.tests.data.janis.simple.scripts' to be distributed and are 2023-09-27T07:48:50,225 already explicitly excluding 'janis_core.tests.data.janis.simple.scripts' via 2023-09-27T07:48:50,226 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,226 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,227 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,228 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,229 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,231 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,231 even if it does not contain any `.py` files. 2023-09-27T07:48:50,232 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,232 directory, all directories are treated like packages. 2023-09-27T07:48:50,233 ******************************************************************************** 2023-09-27T07:48:50,234 !! 2023-09-27T07:48:50,235 check.warn(importable) 2023-09-27T07:48:50,235 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.janis.simple.tools' is absent from the `packages` configuration. 2023-09-27T07:48:50,236 !! 2023-09-27T07:48:50,237 ******************************************************************************** 2023-09-27T07:48:50,238 ############################ 2023-09-27T07:48:50,238 # Package would be ignored # 2023-09-27T07:48:50,239 ############################ 2023-09-27T07:48:50,239 Python recognizes 'janis_core.tests.data.janis.simple.tools' as an importable package[^1], 2023-09-27T07:48:50,240 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,241 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,241 package, please make sure that 'janis_core.tests.data.janis.simple.tools' is explicitly added 2023-09-27T07:48:50,241 to the `packages` configuration field. 2023-09-27T07:48:50,242 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,243 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,243 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,244 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,245 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,246 If you don't want 'janis_core.tests.data.janis.simple.tools' to be distributed and are 2023-09-27T07:48:50,246 already explicitly excluding 'janis_core.tests.data.janis.simple.tools' via 2023-09-27T07:48:50,247 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,247 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,248 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,250 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,257 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,270 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,299 even if it does not contain any `.py` files. 2023-09-27T07:48:50,311 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,313 directory, all directories are treated like packages. 2023-09-27T07:48:50,313 ******************************************************************************** 2023-09-27T07:48:50,314 !! 2023-09-27T07:48:50,315 check.warn(importable) 2023-09-27T07:48:50,315 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.janis.simple_truncated.scripts' is absent from the `packages` configuration. 2023-09-27T07:48:50,316 !! 2023-09-27T07:48:50,317 ******************************************************************************** 2023-09-27T07:48:50,317 ############################ 2023-09-27T07:48:50,318 # Package would be ignored # 2023-09-27T07:48:50,319 ############################ 2023-09-27T07:48:50,319 Python recognizes 'janis_core.tests.data.janis.simple_truncated.scripts' as an importable package[^1], 2023-09-27T07:48:50,320 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,326 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,332 package, please make sure that 'janis_core.tests.data.janis.simple_truncated.scripts' is explicitly added 2023-09-27T07:48:50,337 to the `packages` configuration field. 2023-09-27T07:48:50,338 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,338 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,339 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,340 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,341 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,342 If you don't want 'janis_core.tests.data.janis.simple_truncated.scripts' to be distributed and are 2023-09-27T07:48:50,342 already explicitly excluding 'janis_core.tests.data.janis.simple_truncated.scripts' via 2023-09-27T07:48:50,343 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,343 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,344 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,345 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,345 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,347 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,347 even if it does not contain any `.py` files. 2023-09-27T07:48:50,348 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,348 directory, all directories are treated like packages. 2023-09-27T07:48:50,349 ******************************************************************************** 2023-09-27T07:48:50,350 !! 2023-09-27T07:48:50,350 check.warn(importable) 2023-09-27T07:48:50,351 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.janis.simple_truncated.tools' is absent from the `packages` configuration. 2023-09-27T07:48:50,351 !! 2023-09-27T07:48:50,352 ******************************************************************************** 2023-09-27T07:48:50,353 ############################ 2023-09-27T07:48:50,354 # Package would be ignored # 2023-09-27T07:48:50,354 ############################ 2023-09-27T07:48:50,355 Python recognizes 'janis_core.tests.data.janis.simple_truncated.tools' as an importable package[^1], 2023-09-27T07:48:50,356 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,357 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,357 package, please make sure that 'janis_core.tests.data.janis.simple_truncated.tools' is explicitly added 2023-09-27T07:48:50,365 to the `packages` configuration field. 2023-09-27T07:48:50,371 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,377 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,396 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,412 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,414 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,415 If you don't want 'janis_core.tests.data.janis.simple_truncated.tools' to be distributed and are 2023-09-27T07:48:50,416 already explicitly excluding 'janis_core.tests.data.janis.simple_truncated.tools' via 2023-09-27T07:48:50,416 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,417 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,418 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,419 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,420 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,426 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,428 even if it does not contain any `.py` files. 2023-09-27T07:48:50,429 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,429 directory, all directories are treated like packages. 2023-09-27T07:48:50,430 ******************************************************************************** 2023-09-27T07:48:50,431 !! 2023-09-27T07:48:50,432 check.warn(importable) 2023-09-27T07:48:50,433 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.janis.wgs_somatic_dep' is absent from the `packages` configuration. 2023-09-27T07:48:50,434 !! 2023-09-27T07:48:50,435 ******************************************************************************** 2023-09-27T07:48:50,436 ############################ 2023-09-27T07:48:50,437 # Package would be ignored # 2023-09-27T07:48:50,438 ############################ 2023-09-27T07:48:50,438 Python recognizes 'janis_core.tests.data.janis.wgs_somatic_dep' as an importable package[^1], 2023-09-27T07:48:50,439 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,440 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,441 package, please make sure that 'janis_core.tests.data.janis.wgs_somatic_dep' is explicitly added 2023-09-27T07:48:50,442 to the `packages` configuration field. 2023-09-27T07:48:50,444 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,444 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,445 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,447 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,448 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,449 If you don't want 'janis_core.tests.data.janis.wgs_somatic_dep' to be distributed and are 2023-09-27T07:48:50,450 already explicitly excluding 'janis_core.tests.data.janis.wgs_somatic_dep' via 2023-09-27T07:48:50,451 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,452 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,453 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,454 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,456 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,459 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,460 even if it does not contain any `.py` files. 2023-09-27T07:48:50,460 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,461 directory, all directories are treated like packages. 2023-09-27T07:48:50,463 ******************************************************************************** 2023-09-27T07:48:50,464 !! 2023-09-27T07:48:50,464 check.warn(importable) 2023-09-27T07:48:50,465 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.janis.wgs_somatic_dep.cwl' is absent from the `packages` configuration. 2023-09-27T07:48:50,466 !! 2023-09-27T07:48:50,467 ******************************************************************************** 2023-09-27T07:48:50,468 ############################ 2023-09-27T07:48:50,468 # Package would be ignored # 2023-09-27T07:48:50,469 ############################ 2023-09-27T07:48:50,470 Python recognizes 'janis_core.tests.data.janis.wgs_somatic_dep.cwl' as an importable package[^1], 2023-09-27T07:48:50,471 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,472 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,472 package, please make sure that 'janis_core.tests.data.janis.wgs_somatic_dep.cwl' is explicitly added 2023-09-27T07:48:50,473 to the `packages` configuration field. 2023-09-27T07:48:50,474 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,475 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,475 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,477 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,478 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,479 If you don't want 'janis_core.tests.data.janis.wgs_somatic_dep.cwl' to be distributed and are 2023-09-27T07:48:50,480 already explicitly excluding 'janis_core.tests.data.janis.wgs_somatic_dep.cwl' via 2023-09-27T07:48:50,480 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,481 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,481 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,482 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,483 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,485 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,485 even if it does not contain any `.py` files. 2023-09-27T07:48:50,486 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,486 directory, all directories are treated like packages. 2023-09-27T07:48:50,487 ******************************************************************************** 2023-09-27T07:48:50,488 !! 2023-09-27T07:48:50,488 check.warn(importable) 2023-09-27T07:48:50,489 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.janis.wgs_somatic_dep.cwl.tools' is absent from the `packages` configuration. 2023-09-27T07:48:50,489 !! 2023-09-27T07:48:50,490 ******************************************************************************** 2023-09-27T07:48:50,491 ############################ 2023-09-27T07:48:50,491 # Package would be ignored # 2023-09-27T07:48:50,491 ############################ 2023-09-27T07:48:50,492 Python recognizes 'janis_core.tests.data.janis.wgs_somatic_dep.cwl.tools' as an importable package[^1], 2023-09-27T07:48:50,493 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,494 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,494 package, please make sure that 'janis_core.tests.data.janis.wgs_somatic_dep.cwl.tools' is explicitly added 2023-09-27T07:48:50,495 to the `packages` configuration field. 2023-09-27T07:48:50,496 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,496 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,497 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,498 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,499 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,500 If you don't want 'janis_core.tests.data.janis.wgs_somatic_dep.cwl.tools' to be distributed and are 2023-09-27T07:48:50,501 already explicitly excluding 'janis_core.tests.data.janis.wgs_somatic_dep.cwl.tools' via 2023-09-27T07:48:50,501 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,502 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,502 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,503 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,504 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,505 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,506 even if it does not contain any `.py` files. 2023-09-27T07:48:50,506 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,506 directory, all directories are treated like packages. 2023-09-27T07:48:50,507 ******************************************************************************** 2023-09-27T07:48:50,508 !! 2023-09-27T07:48:50,508 check.warn(importable) 2023-09-27T07:48:50,509 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.janis.wgs_somatic_dep.wdl' is absent from the `packages` configuration. 2023-09-27T07:48:50,509 !! 2023-09-27T07:48:50,510 ******************************************************************************** 2023-09-27T07:48:50,510 ############################ 2023-09-27T07:48:50,511 # Package would be ignored # 2023-09-27T07:48:50,511 ############################ 2023-09-27T07:48:50,512 Python recognizes 'janis_core.tests.data.janis.wgs_somatic_dep.wdl' as an importable package[^1], 2023-09-27T07:48:50,512 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,513 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,514 package, please make sure that 'janis_core.tests.data.janis.wgs_somatic_dep.wdl' is explicitly added 2023-09-27T07:48:50,514 to the `packages` configuration field. 2023-09-27T07:48:50,516 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,517 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,517 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,518 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,519 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,520 If you don't want 'janis_core.tests.data.janis.wgs_somatic_dep.wdl' to be distributed and are 2023-09-27T07:48:50,521 already explicitly excluding 'janis_core.tests.data.janis.wgs_somatic_dep.wdl' via 2023-09-27T07:48:50,521 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,521 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,522 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,523 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,524 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,525 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,526 even if it does not contain any `.py` files. 2023-09-27T07:48:50,526 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,527 directory, all directories are treated like packages. 2023-09-27T07:48:50,528 ******************************************************************************** 2023-09-27T07:48:50,529 !! 2023-09-27T07:48:50,529 check.warn(importable) 2023-09-27T07:48:50,530 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.janis.wgs_somatic_dep.wdl.tools' is absent from the `packages` configuration. 2023-09-27T07:48:50,530 !! 2023-09-27T07:48:50,531 ******************************************************************************** 2023-09-27T07:48:50,531 ############################ 2023-09-27T07:48:50,532 # Package would be ignored # 2023-09-27T07:48:50,532 ############################ 2023-09-27T07:48:50,533 Python recognizes 'janis_core.tests.data.janis.wgs_somatic_dep.wdl.tools' as an importable package[^1], 2023-09-27T07:48:50,533 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,534 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,534 package, please make sure that 'janis_core.tests.data.janis.wgs_somatic_dep.wdl.tools' is explicitly added 2023-09-27T07:48:50,535 to the `packages` configuration field. 2023-09-27T07:48:50,536 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,536 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,537 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,538 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,539 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,540 If you don't want 'janis_core.tests.data.janis.wgs_somatic_dep.wdl.tools' to be distributed and are 2023-09-27T07:48:50,540 already explicitly excluding 'janis_core.tests.data.janis.wgs_somatic_dep.wdl.tools' via 2023-09-27T07:48:50,541 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,541 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,542 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,543 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,544 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,546 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,546 even if it does not contain any `.py` files. 2023-09-27T07:48:50,547 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,547 directory, all directories are treated like packages. 2023-09-27T07:48:50,548 ******************************************************************************** 2023-09-27T07:48:50,549 !! 2023-09-27T07:48:50,549 check.warn(importable) 2023-09-27T07:48:50,550 /tmp/pip-build-env-rwc1kdsn/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'janis_core.tests.data.wdl' is absent from the `packages` configuration. 2023-09-27T07:48:50,551 !! 2023-09-27T07:48:50,552 ******************************************************************************** 2023-09-27T07:48:50,552 ############################ 2023-09-27T07:48:50,553 # Package would be ignored # 2023-09-27T07:48:50,553 ############################ 2023-09-27T07:48:50,554 Python recognizes 'janis_core.tests.data.wdl' as an importable package[^1], 2023-09-27T07:48:50,554 but it is absent from setuptools' `packages` configuration. 2023-09-27T07:48:50,557 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-27T07:48:50,557 package, please make sure that 'janis_core.tests.data.wdl' is explicitly added 2023-09-27T07:48:50,558 to the `packages` configuration field. 2023-09-27T07:48:50,560 Alternatively, you can also rely on setuptools' discovery methods 2023-09-27T07:48:50,561 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-27T07:48:50,562 instead of `find_packages(...)`/`find:`). 2023-09-27T07:48:50,563 You can read more about "package discovery" on setuptools documentation page: 2023-09-27T07:48:50,564 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-27T07:48:50,565 If you don't want 'janis_core.tests.data.wdl' to be distributed and are 2023-09-27T07:48:50,566 already explicitly excluding 'janis_core.tests.data.wdl' via 2023-09-27T07:48:50,566 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-27T07:48:50,567 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-27T07:48:50,567 combination with a more fine grained `package-data` configuration. 2023-09-27T07:48:50,569 You can read more about "package data files" on setuptools documentation page: 2023-09-27T07:48:50,570 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-27T07:48:50,571 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-27T07:48:50,572 even if it does not contain any `.py` files. 2023-09-27T07:48:50,573 On the other hand, currently there is no concept of package data 2023-09-27T07:48:50,573 directory, all directories are treated like packages. 2023-09-27T07:48:50,574 ******************************************************************************** 2023-09-27T07:48:50,575 !! 2023-09-27T07:48:50,575 check.warn(importable) 2023-09-27T07:48:50,576 copying janis_core/messages/config.yaml -> build/lib/janis_core/messages 2023-09-27T07:48:50,577 creating build/lib/janis_core/ingestion/data 2023-09-27T07:48:50,577 copying janis_core/ingestion/data/logging_config.yaml -> build/lib/janis_core/ingestion/data 2023-09-27T07:48:50,578 copying janis_core/ingestion/data/janis_types.yaml -> build/lib/janis_core/ingestion/data 2023-09-27T07:48:50,579 creating build/lib/janis_core/ingestion/data/galaxy 2023-09-27T07:48:50,579 copying janis_core/ingestion/data/galaxy/galaxy_config.yaml -> build/lib/janis_core/ingestion/data/galaxy 2023-09-27T07:48:50,580 copying janis_core/ingestion/data/galaxy/datatypes_conf.xml.sample -> build/lib/janis_core/ingestion/data/galaxy 2023-09-27T07:48:50,580 creating build/lib/janis_core/tests/data 2023-09-27T07:48:50,581 copying janis_core/tests/data/aln.sam -> build/lib/janis_core/tests/data 2023-09-27T07:48:50,582 copying janis_core/tests/data/aln.sorted.bam -> build/lib/janis_core/tests/data 2023-09-27T07:48:50,582 copying janis_core/tests/data/aln.sorted.bam.bai -> build/lib/janis_core/tests/data 2023-09-27T07:48:50,583 copying janis_core/tests/data/mutant_R1.fastq -> build/lib/janis_core/tests/data 2023-09-27T07:48:50,583 copying janis_core/tests/data/test.txt -> build/lib/janis_core/tests/data 2023-09-27T07:48:50,584 copying janis_core/tests/data/test_diff.txt -> build/lib/janis_core/tests/data 2023-09-27T07:48:50,585 copying janis_core/tests/data/wildtype.fna -> build/lib/janis_core/tests/data 2023-09-27T07:48:50,585 creating build/lib/janis_core/tests/data/cwl 2023-09-27T07:48:50,586 creating build/lib/janis_core/tests/data/cwl/tools 2023-09-27T07:48:50,586 copying janis_core/tests/data/cwl/tools/BasicTestTool.cwl -> build/lib/janis_core/tests/data/cwl/tools 2023-09-27T07:48:50,587 copying janis_core/tests/data/cwl/tools/bwamem.cwl -> build/lib/janis_core/tests/data/cwl/tools 2023-09-27T07:48:50,587 copying janis_core/tests/data/cwl/tools/echo.cwl -> build/lib/janis_core/tests/data/cwl/tools 2023-09-27T07:48:50,588 copying janis_core/tests/data/cwl/tools/fastqc.cwl -> build/lib/janis_core/tests/data/cwl/tools 2023-09-27T07:48:50,589 copying janis_core/tests/data/cwl/tools/fastqc2.cwl -> build/lib/janis_core/tests/data/cwl/tools 2023-09-27T07:48:50,589 copying janis_core/tests/data/cwl/tools/gatk_haplotype_caller.cwl -> build/lib/janis_core/tests/data/cwl/tools 2023-09-27T07:48:50,590 copying janis_core/tests/data/cwl/tools/gatk_haplotype_caller_long.cwl -> build/lib/janis_core/tests/data/cwl/tools 2023-09-27T07:48:50,590 copying janis_core/tests/data/cwl/tools/rename_png.cwl -> build/lib/janis_core/tests/data/cwl/tools 2023-09-27T07:48:50,591 copying janis_core/tests/data/cwl/tools/rose.cwl -> build/lib/janis_core/tests/data/cwl/tools 2023-09-27T07:48:50,591 copying janis_core/tests/data/cwl/tools/samtools_flagstat.cwl -> build/lib/janis_core/tests/data/cwl/tools 2023-09-27T07:48:50,592 creating build/lib/janis_core/tests/data/cwl/tools/datatypes 2023-09-27T07:48:50,592 copying janis_core/tests/data/cwl/tools/datatypes/array_types.cwl -> build/lib/janis_core/tests/data/cwl/tools/datatypes 2023-09-27T07:48:50,593 copying janis_core/tests/data/cwl/tools/datatypes/basic_types.cwl -> build/lib/janis_core/tests/data/cwl/tools/datatypes 2023-09-27T07:48:50,593 copying janis_core/tests/data/cwl/tools/datatypes/secondary_types.cwl -> build/lib/janis_core/tests/data/cwl/tools/datatypes 2023-09-27T07:48:50,594 creating build/lib/janis_core/tests/data/cwl/tools/expressions 2023-09-27T07:48:50,594 copying janis_core/tests/data/cwl/tools/expressions/inputs_arguments.cwl -> build/lib/janis_core/tests/data/cwl/tools/expressions 2023-09-27T07:48:50,595 copying janis_core/tests/data/cwl/tools/expressions/outputs.cwl -> build/lib/janis_core/tests/data/cwl/tools/expressions 2023-09-27T07:48:50,595 copying janis_core/tests/data/cwl/tools/expressions/requirements.cwl -> build/lib/janis_core/tests/data/cwl/tools/expressions 2023-09-27T07:48:50,596 copying janis_core/tests/data/cwl/tools/expressions/resources.cwl -> build/lib/janis_core/tests/data/cwl/tools/expressions 2023-09-27T07:48:50,596 copying janis_core/tests/data/cwl/tools/expressions/streams.cwl -> build/lib/janis_core/tests/data/cwl/tools/expressions 2023-09-27T07:48:50,597 creating build/lib/janis_core/tests/data/cwl/tools/expressiontools 2023-09-27T07:48:50,597 copying janis_core/tests/data/cwl/tools/expressiontools/check_value.cwl -> build/lib/janis_core/tests/data/cwl/tools/expressiontools 2023-09-27T07:48:50,598 creating build/lib/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:50,598 copying janis_core/tests/data/cwl/tools/requirements/add_crossmapped2resmapped.cwl -> build/lib/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:50,599 copying janis_core/tests/data/cwl/tools/requirements/amplicon_architect.cwl -> build/lib/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:50,600 copying janis_core/tests/data/cwl/tools/requirements/antismash_v4.cwl -> build/lib/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:50,600 copying janis_core/tests/data/cwl/tools/requirements/bundle_secondaryfiles.cwl -> build/lib/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:50,601 copying janis_core/tests/data/cwl/tools/requirements/check_threshold.cwl -> build/lib/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:50,601 copying janis_core/tests/data/cwl/tools/requirements/control-freec-11-6-sbg.cwl -> build/lib/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:50,602 copying janis_core/tests/data/cwl/tools/requirements/prepare_fasta_db.cwl -> build/lib/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:50,603 copying janis_core/tests/data/cwl/tools/requirements/return_directory.cwl -> build/lib/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:50,603 creating build/lib/janis_core/tests/data/cwl/tools/requirements/Python 2023-09-27T07:48:50,604 copying janis_core/tests/data/cwl/tools/requirements/Python/add_crossmapped2resmapped.py -> build/lib/janis_core/tests/data/cwl/tools/requirements/Python 2023-09-27T07:48:50,604 copying janis_core/tests/data/cwl/tools/requirements/Python/check_threshold.py -> build/lib/janis_core/tests/data/cwl/tools/requirements/Python 2023-09-27T07:48:50,605 creating build/lib/janis_core/tests/data/cwl/workflows 2023-09-27T07:48:50,606 copying janis_core/tests/data/cwl/workflows/expressions.cwl -> build/lib/janis_core/tests/data/cwl/workflows 2023-09-27T07:48:50,606 copying janis_core/tests/data/cwl/workflows/super_enhancer_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows 2023-09-27T07:48:50,607 creating build/lib/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:48:50,607 copying janis_core/tests/data/cwl/workflows/CroMaSt/CONTRIBUTING.md -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:48:50,608 copying janis_core/tests/data/cwl/workflows/CroMaSt/CroMaSt.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:48:50,608 copying janis_core/tests/data/cwl/workflows/CroMaSt/LICENSE -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:48:50,609 copying janis_core/tests/data/cwl/workflows/CroMaSt/README.md -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:48:50,610 copying janis_core/tests/data/cwl/workflows/CroMaSt/ro-crate-metadata.json -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:48:50,610 copying janis_core/tests/data/cwl/workflows/CroMaSt/ro-crate-preview.html -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:48:50,611 copying janis_core/tests/data/cwl/workflows/CroMaSt/workflow-390-9f3832867eab6c7a6363f8ca594a4bcf2ff7e96f-diagram.svg -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:48:50,611 creating build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,612 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/add_crossmapped2resmapped.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,612 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/add_domain_num.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,613 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/align_compute_avg.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,613 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/check_threshold.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,614 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/chop_struct2domains.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,615 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/compare_cath_pfam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,615 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/core_avg_subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,616 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/create_param.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,617 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/crossmapped_per_unp_dom.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,617 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/download_data.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,618 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/filter_align_scores.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,619 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/gather_lost_resmap.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,619 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/get_family_ids.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,620 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/list_true_domains.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,621 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/map_unique_struct_cath2pfam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,621 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/map_unique_struct_pfam2cath.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,622 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/merge_df2json.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,623 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/move_files.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,623 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/other_avg_subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,624 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/pairwise_aligner.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,624 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/resmapping_cath2up.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,626 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/resmapping_cath_instances_subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,628 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/resmapping_pfam2pdb.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,631 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/resmapping_pfam_instances_subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,633 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/separate_cath.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,636 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/separate_pfam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,639 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/unmapped_unp_avg_align.cwl -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:48:50,641 creating build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,642 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/add_crossmapped2resmapped.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,645 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/add_domain_num.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,648 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/align_compute_avg.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,651 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/check_threshold.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,656 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/chop_struct2domains.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,659 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/compare_cath_pfam.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,662 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/create_param.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,664 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/crossmapped_per_unp_dom.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,667 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/filter_align_scores.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,669 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/get_family_ids.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,671 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/map_unique_struct_cath2pfam.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,674 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/map_unique_struct_pfam2cath.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,676 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/merge_df2json.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,678 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/pairwise_aligner.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,681 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/residue_mapping.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,683 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/resmapping_cath2up.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,686 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/resmapping_pfam2pdb.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,688 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/separate_cath.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,691 copying janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/separate_pfam.py -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:48:50,693 creating build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/translated 2023-09-27T07:48:50,694 copying janis_core/tests/data/cwl/workflows/CroMaSt/translated/main.nf -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/translated 2023-09-27T07:48:50,696 creating build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/yml 2023-09-27T07:48:50,697 copying janis_core/tests/data/cwl/workflows/CroMaSt/yml/CroMaSt_input.yml -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/yml 2023-09-27T07:48:50,699 copying janis_core/tests/data/cwl/workflows/CroMaSt/yml/download_data.yml -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/yml 2023-09-27T07:48:50,701 copying janis_core/tests/data/cwl/workflows/CroMaSt/yml/environment.yml -> build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/yml 2023-09-27T07:48:50,704 creating build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup 2023-09-27T07:48:50,705 copying janis_core/tests/data/cwl/workflows/align_sort_markdup/align_sort_markdup.cwl -> build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup 2023-09-27T07:48:50,707 creating build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/subworkflows 2023-09-27T07:48:50,708 copying janis_core/tests/data/cwl/workflows/align_sort_markdup/subworkflows/align.cwl -> build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/subworkflows 2023-09-27T07:48:50,710 creating build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools 2023-09-27T07:48:50,711 copying janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/align_and_tag.cwl -> build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools 2023-09-27T07:48:50,713 copying janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/index_bam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools 2023-09-27T07:48:50,715 copying janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/mark_duplicates_and_sort.cwl -> build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools 2023-09-27T07:48:50,718 copying janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/merge_bams_samtools.cwl -> build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools 2023-09-27T07:48:50,720 copying janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/name_sort.cwl -> build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools 2023-09-27T07:48:50,722 creating build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows 2023-09-27T07:48:50,722 creating build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/pipelines 2023-09-27T07:48:50,723 copying janis_core/tests/data/cwl/workflows/analysis-workflows/pipelines/alignment_exome.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/pipelines 2023-09-27T07:48:50,726 creating build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:48:50,727 copying janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/align.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:48:50,729 copying janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/align_sort_markdup.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:48:50,731 copying janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/hs_metrics.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:48:50,733 copying janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/qc_exome.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:48:50,736 copying janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/sequence_align_and_tag_adapter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:48:50,738 copying janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/sequence_to_bqsr.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:48:50,741 creating build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,742 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/align_and_tag.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,745 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/apply_bqsr.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,747 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/bqsr.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,750 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/collect_alignment_summary_metrics.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,752 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/collect_hs_metrics.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,754 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/collect_insert_size_metrics.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,756 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/gatk_haplotype_caller.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,758 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/index_bam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,760 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/mark_duplicates_and_sort.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,763 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/merge_bams.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,765 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/merge_bams_samtools.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,767 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/name_sort.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,769 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/samtools_flagstat.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,771 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/select_variants.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,773 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/sequence_align_and_tag.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,775 copying janis_core/tests/data/cwl/workflows/analysis-workflows/tools/verify_bam_id.cwl -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:48:50,777 creating build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/types 2023-09-27T07:48:50,778 copying janis_core/tests/data/cwl/workflows/analysis-workflows/types/labelled_file.yml -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/types 2023-09-27T07:48:50,781 copying janis_core/tests/data/cwl/workflows/analysis-workflows/types/sequence_data.yml -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/types 2023-09-27T07:48:50,783 copying janis_core/tests/data/cwl/workflows/analysis-workflows/types/trimming_options.yml -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/types 2023-09-27T07:48:50,785 copying janis_core/tests/data/cwl/workflows/analysis-workflows/types/vep_custom_annotation.yml -> build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/types 2023-09-27T07:48:50,787 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics 2023-09-27T07:48:50,787 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools 2023-09-27T07:48:50,788 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly 2023-09-27T07:48:50,789 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,790 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-output_formats.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,792 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-strand_values.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,794 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastp-v0.9.21.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,796 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastp-v0.9.21.test.job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,799 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastp-v0.9.21_docker.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,801 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastx-v0.9.21.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,804 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastx-v0.9.21.test.job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,806 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.makedb-v0.9.21.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,808 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.makedb-v0.9.21.test.job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,810 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond_blastp_test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,812 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond_blastx_test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,814 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/diamond-subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,816 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/diamond-subwf.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:48:50,818 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:48:50,819 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:48:50,821 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_join.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:48:50,823 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_join.job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:48:50,825 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_join.test.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:48:50,827 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_post_run_join.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:48:50,829 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_sorting.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:48:50,831 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_sorting.job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:48:50,833 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_sorting.test.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:48:50,835 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/postprocessing_subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:48:50,837 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/postprocessing_subwf.job.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:48:50,840 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/postprocessing_subwf.test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:48:50,842 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files 2023-09-27T07:48:50,843 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/example_diamond_10 -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files 2023-09-27T07:48:50,845 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/example_diamond_10_sorted -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files 2023-09-27T07:48:50,847 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/example_diamond_db -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files 2023-09-27T07:48:50,849 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/output_example 2023-09-27T07:48:50,850 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/output_example/example_diamond_10_sorted_join -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/output_example 2023-09-27T07:48:50,853 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG 2023-09-27T07:48:50,854 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggnog-subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG 2023-09-27T07:48:50,857 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggnog-subwf.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG 2023-09-27T07:48:50,859 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG 2023-09-27T07:48:50,860 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG 2023-09-27T07:48:50,862 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnog.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG 2023-09-27T07:48:50,864 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnog.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG 2023-09-27T07:48:50,866 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/emapper.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG 2023-09-27T07:48:50,869 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:48:50,870 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/__init__.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:48:50,872 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/annota.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:48:50,875 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/annota_mongo.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:48:50,878 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/common.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:48:50,880 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/orthology.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:48:50,883 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/search.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:48:50,886 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/seqio.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:48:50,888 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/server.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:48:50,890 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/utils.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:48:50,893 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/vars.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:48:50,897 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/version.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:48:50,899 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF 2023-09-27T07:48:50,900 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF/build_assembly_gff.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF 2023-09-27T07:48:50,902 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF/gff_generation.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF 2023-09-27T07:48:50,905 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF/gff_generation.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF 2023-09-27T07:48:50,907 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties 2023-09-27T07:48:50,908 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties 2023-09-27T07:48:50,910 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/genome_properties.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties 2023-09-27T07:48:50,912 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/genome_properties.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties 2023-09-27T07:48:50,915 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/gp_docker.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties 2023-09-27T07:48:50,917 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output 2023-09-27T07:48:50,918 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output/JSON_test_single_protein.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output 2023-09-27T07:48:50,943 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output/LONGFORM_REPORT_test_single_protein.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output 2023-09-27T07:48:50,962 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output/MATCHES_test_single_protein.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output 2023-09-27T07:48:50,963 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output/SUMMARY_FILE_test_single_protein.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output 2023-09-27T07:48:50,968 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output/TABLE_test_single_protein.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output 2023-09-27T07:48:50,978 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/test-input 2023-09-27T07:48:50,979 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/test-input/InterProScan.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/test-input 2023-09-27T07:48:50,982 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis 2023-09-27T07:48:50,983 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/make_graphs.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis 2023-09-27T07:48:50,985 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker 2023-09-27T07:48:50,986 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker 2023-09-27T07:48:50,988 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker/help_commands.txt -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker 2023-09-27T07:48:50,991 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker/run_pathways.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker 2023-09-27T07:48:50,993 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways 2023-09-27T07:48:50,994 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways/give_pathways.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways 2023-09-27T07:48:50,996 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways/kegg_pathways.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways 2023-09-27T07:48:50,999 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways/kegg_pathways.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways 2023-09-27T07:48:51,001 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Modification 2023-09-27T07:48:51,002 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Modification/modification_table.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Modification 2023-09-27T07:48:51,004 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Modification/modification_table.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Modification 2023-09-27T07:48:51,006 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan 2023-09-27T07:48:51,007 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan/parsing_hmmscan.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan 2023-09-27T07:48:51,009 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan/parsing_hmmscan.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan 2023-09-27T07:48:51,011 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan/parsing_hmmscan.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan 2023-09-27T07:48:51,013 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/expected-output 2023-09-27T07:48:51,014 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/expected-output/assembly-SRR1620013_small_FASTA_FASTA.summary.kegg_contigs.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/expected-output 2023-09-27T07:48:51,016 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/expected-output/assembly-SRR1620013_small_FASTA_FASTA.summary.kegg_pathways -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/expected-output 2023-09-27T07:48:51,018 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Viral 2023-09-27T07:48:51,019 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Viral/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Viral 2023-09-27T07:48:51,021 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash 2023-09-27T07:48:51,022 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals 2023-09-27T07:48:51,023 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash_chunking_subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals 2023-09-27T07:48:51,025 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash_subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals 2023-09-27T07:48:51,027 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/filtering_fasta_for_antismash.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals 2023-09-27T07:48:51,030 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/no_antismash_subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals 2023-09-27T07:48:51,032 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/wf_antismash.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals 2023-09-27T07:48:51,034 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash 2023-09-27T07:48:51,035 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash/antismash_v4.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash 2023-09-27T07:48:51,037 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash/antismash_v4.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash 2023-09-27T07:48:51,039 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash/run_antismash_short.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash 2023-09-27T07:48:51,041 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/check_value 2023-09-27T07:48:51,042 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/check_value/check_value.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/check_value 2023-09-27T07:48:51,044 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/check_value/check_value.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/check_value 2023-09-27T07:48:51,046 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing 2023-09-27T07:48:51,046 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk 2023-09-27T07:48:51,047 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk/change_antismash_output.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk 2023-09-27T07:48:51,050 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk/change_output.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk 2023-09-27T07:48:51,052 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk/change_output.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk 2023-09-27T07:48:51,054 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_geneclusters_txt 2023-09-27T07:48:51,055 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_geneclusters_txt/change_geneclusters_ctg.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_geneclusters_txt 2023-09-27T07:48:51,057 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_geneclusters_txt/change_geneclusters_txt.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_geneclusters_txt 2023-09-27T07:48:51,059 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash 2023-09-27T07:48:51,060 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash/antismash_to_gff.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash 2023-09-27T07:48:51,062 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash/antismash_to_gff.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash 2023-09-27T07:48:51,065 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash/antismash_to_gff.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash 2023-09-27T07:48:51,067 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/reformat_antismash 2023-09-27T07:48:51,068 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/reformat_antismash/reformat_antismash.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/reformat_antismash 2023-09-27T07:48:51,070 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/reformat_antismash/reformat_antismash.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/reformat_antismash 2023-09-27T07:48:51,072 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs 2023-09-27T07:48:51,073 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs/antismash_rename_contigs.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs 2023-09-27T07:48:51,075 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs/rename_contigs.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs 2023-09-27T07:48:51,077 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs/rename_contigs.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs 2023-09-27T07:48:51,079 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:48:51,080 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input/empty.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:48:51,082 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input/test-1-contig.embl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:48:51,102 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input/test-1-contig.table -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:48:51,105 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input/test.2.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:48:51,107 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input/test.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:48:51,110 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input/test.fasta.1 -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:48:51,112 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-output 2023-09-27T07:48:51,114 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-output/output-contig-1.embl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-output 2023-09-27T07:48:51,132 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-output/output-contig-1.gbk -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-output 2023-09-27T07:48:51,152 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated 2023-09-27T07:48:51,154 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/config -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated 2023-09-27T07:48:51,156 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/main.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated 2023-09-27T07:48:51,160 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,162 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/FGS.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,165 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/QC_FLAG.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,167 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/add_crossmapped_to_resmapped.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,170 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/add_domain_positions.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,172 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/add_island_names.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,175 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/align_avg_structs_pairwise.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,177 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/assign_genes.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,179 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/avg_averaged_structures.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,182 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/avg_averaged_unp_domains.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,184 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/avg_chopped_structs_unp_domains.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,187 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/avg_chopped_structures_unp_domains.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,189 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bam_index.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,192 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bed_to_bigbed.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,195 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bed_to_macs.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,197 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bundle_secondaries.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,200 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bwa_index.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,204 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/carveme.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,206 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/carveme_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,209 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/cat.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,211 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/cat_models.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,213 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/check_alignment_scores.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,216 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/check_threshold_step.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,218 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chinking_SC_fasta_nucleotide.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,221 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chinking_fasta_nucleotide.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,223 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chinking_fasta_proteins.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,226 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chop_structs.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,228 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chunking_tsv.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,231 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/classifications_to_otu_counts.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,234 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/clean_classification.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,237 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/clean_fasta_headers.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,239 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/cmsearch.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,243 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/collect_lost_instances.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,246 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/combine.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,249 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/combine_ips.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,252 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/combine_trimmed.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,254 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compare_instances_CATH_Pfam.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,257 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compress.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,259 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compress_carveme.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,262 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compress_mapseq.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,265 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compress_prodigal.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,267 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compression.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,270 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/conversion.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,272 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/convert_trimmed_reads_to_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,275 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/copy_avg_dom.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,277 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_ITS_seqs.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,280 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_cds.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,283 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_lines_mapseq.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,286 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_lsu_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,289 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_masked_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,291 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_overlapped_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,294 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_processed_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,297 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_ssu_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,299 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_submitted_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,302 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_submitted_reads_single.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,304 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/counts_to_hdf5.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,306 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/counts_to_json.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,309 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/create_new_parameters.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,311 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/crossmapping_CATH2Pfam.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,314 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/crossmapping_Pfam2CATH.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,316 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/expressiontool_bam_index.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,319 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/extract_coords.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,321 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/extract_sequences.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,324 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/extract_subunits.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,326 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/extract_subunits_coords.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,329 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/fastqc.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,331 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/fastqc_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,334 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/filter_cath_structures.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,336 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/filter_paired.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,339 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/filter_pfam_structures.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,341 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/folder_compression.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,344 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/format_core_list.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,346 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/functional_stats.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,349 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gather_domain_like.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,351 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gather_failed_domains.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,354 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gatk_selectvariants_manta.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,356 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gemstats.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,359 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/get_coords.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,362 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/get_family_ids.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,364 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/get_ncrnas.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,366 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/go_summary.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,369 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,371 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip_LSU.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,374 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip_SSU.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,376 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip_files.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,378 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip_masked_ITS.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,381 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/hashsum_paired.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,383 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/hashsum_single.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,386 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/header_addition.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,388 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/hmmsearch.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,391 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/index_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,394 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/index_strelka_bed.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,396 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/interproscan.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,399 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/kofamscan.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,401 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/length_filter.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,403 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/make_gff.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,406 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/make_tab_sep.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,408 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/manta.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,411 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/mapseq.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,414 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/mask_for_ITS.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,416 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/memote_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,418 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/memote_report_snapshot.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,421 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/memote_run.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,424 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/motus_classification.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,426 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/move_to_functional_annotation_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,428 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/move_to_seq_cat_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,431 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/ngtax.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,434 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/ngtax_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,436 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/ngtax_to_tsv_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,439 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/no_tax_file_flag.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,442 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/overlap_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,444 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/pairwise_align_avg_structs.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,447 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/per_dom_instance.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,450 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/per_unp_dom_instance.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,453 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/pfam.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,455 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/phyloseq_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,458 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/picard_create_sequence_dictionary.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,460 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/picrust2.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,463 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/picrust_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,466 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/pilon.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,468 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/post_processing.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,471 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/prodigal.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,473 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/prodigal_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,476 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/qc_stats.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,479 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/readmapping_pilon.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,481 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/reads_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,484 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/reduce_bed.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,487 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/reformat_coords.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,489 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/remove_overlaps.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,492 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/rename_manta_samples.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,494 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/rename_ncrnas.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,497 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/rename_png.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,499 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/resmapping_for_CATH_PDB2UP.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,502 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/resmapping_for_Pfam_UP2PDB.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,505 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/return_its_dir.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,507 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/return_output_dir.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,510 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/return_seq_dir.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,512 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/return_tax_dir.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,515 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/run_concatenate_deoverlapped_matches.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,518 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/run_concatenate_matches.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,520 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/run_quality_control_filtering.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,523 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/run_rose.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,525 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/sam_to_sorted_bam.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,528 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/samtools_faidx.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,530 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/smetana.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,533 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/sort_bed.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,535 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/split_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,538 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/split_seqs.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,540 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/suppress_tax.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,543 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/tohdt.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,546 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/touch_empty_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,549 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/touch_file_flag.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,551 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/touch_no_cds_flag.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,554 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/trim_quality_control.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,556 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/unzip_merged_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,559 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/unzip_single_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,561 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/vcf_compress.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,564 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/visualize_otu_counts.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,566 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/write_summaries.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:48:51,569 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,570 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/ITS.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,573 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/after_qc.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,576 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/avg_unp_domains.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,579 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/before_qc.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,582 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/cath_domain_instances.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,585 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/cgc.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,587 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/chop_and_avg_for_CATH2Pfam.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,590 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/chop_and_avg_for_Pfam2CATH.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,592 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/chop_and_avg_for_core.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,595 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/chop_and_avg_from_list.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,597 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/chunking_final.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,600 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/classify_LSUs.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,603 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/classify_SSUs.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,605 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/cmsearch_assembly.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,608 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/cmsearch_raw_data.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,611 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/combined_gene_caller.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,613 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/find_ribosomal_ncRNAs.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,616 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/functional_annotation.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,618 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/functional_annotation_and_post_processing.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,621 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/motus_taxonomy.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,623 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/other_ncrnas.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,626 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/overlap_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,628 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/pfam_domain_instances.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,631 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/prepare_reference.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,634 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/resmapping_cath_structs.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,636 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/resmapping_pfam_structs.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,639 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/rna_prediction.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,642 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/run_IPS.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,645 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/run_hmmer.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,648 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/run_itsonedb.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,650 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/run_manta.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,653 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/run_unite.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,656 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/trimming.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,658 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/unmapped_from_cath.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,661 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/unmapped_from_pfam.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,664 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/write_summaries.nf -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:48:51,666 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls 2023-09-27T07:48:51,668 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls/antismash_chunking_subwf.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls 2023-09-27T07:48:51,671 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls/antismash_subwf.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls 2023-09-27T07:48:51,673 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls/no_antismash_subwf.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls 2023-09-27T07:48:51,676 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls/wf_antismash.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls 2023-09-27T07:48:51,678 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/move_antismash_summary 2023-09-27T07:48:51,680 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/move_antismash_summary/move_antismash_summary.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/move_antismash_summary 2023-09-27T07:48:51,682 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/move_antismash_summary/move_antismash_summary.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/move_antismash_summary 2023-09-27T07:48:51,685 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta 2023-09-27T07:48:51,686 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta/fasta_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta 2023-09-27T07:48:51,689 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta/fasta_index.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta 2023-09-27T07:48:51,692 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta/run_samtools.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta 2023-09-27T07:48:51,694 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta/test-input 2023-09-27T07:48:51,696 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta/test-input/test.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta/test-input 2023-09-27T07:48:51,699 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:48:51,701 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/FGS.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:48:51,704 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/FGS.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:48:51,706 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/faselector -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:48:51,709 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/post-processing.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:48:51,711 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/predict_proteins_assemblies.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:48:51,713 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/predict_proteins_assemblies.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:48:51,716 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/predict_proteins_reads.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:48:51,718 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/prodigal.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:48:51,720 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/run_FGS.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:48:51,723 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/unite_protein_predictions.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:48:51,726 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:48:51,727 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:48:51,729 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/combined_gene_caller.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:48:51,731 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/combined_gene_caller.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:48:51,734 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/combined_gene_caller.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:48:51,736 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/combined_gene_caller_conf.json -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:48:51,738 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/combined_gene_caller_docker.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:48:51,741 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:48:51,743 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:48:52,010 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.fgs.faa -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:48:52,107 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.fgs.ffn -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:48:52,368 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.prodigal -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:48:52,376 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.prodigal.faa -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:48:52,387 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.prodigal.ffn -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:48:52,405 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/ERR3414571_FASTA.cmsearch.all.tblout.deoverlapped -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:48:52,433 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:48:52,434 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:48:52,436 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go-basic-metagenomics_release_20160705.obo -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:48:53,260 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go-basic-metagenomics_release_20160705.txt -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:48:53,789 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go_summary-config.json -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:48:53,791 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go_summary.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:48:53,794 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go_summary.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:48:53,796 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go_summary_pipeline-1.0.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:48:53,800 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/metagenomics_go_slim_banding.txt -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:48:53,803 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/metagenomics_go_slim_ids.txt -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:48:53,805 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/expected-output 2023-09-27T07:48:53,806 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/expected-output/test -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/expected-output 2023-09-27T07:48:53,809 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/expected-output/test_slim -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/expected-output 2023-09-27T07:48:53,812 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools 2023-09-27T07:48:53,813 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools/owltools -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools 2023-09-27T07:48:53,816 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools/owltools-runner-all.jar -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools 2023-09-27T07:48:54,314 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools/owltools.vmoptions -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools 2023-09-27T07:48:54,316 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/test-input 2023-09-27T07:48:54,317 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/test-input/ips_out.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/test-input 2023-09-27T07:48:54,321 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan 2023-09-27T07:48:54,322 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-apps.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan 2023-09-27T07:48:54,324 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-protein_formats.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan 2023-09-27T07:48:54,326 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-v5-none_docker.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan 2023-09-27T07:48:54,328 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-v5.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan 2023-09-27T07:48:54,330 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-v5.test.job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan 2023-09-27T07:48:54,333 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse 2023-09-27T07:48:54,334 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/pfam_annotations.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse 2023-09-27T07:48:54,336 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/pfam_annotations.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse 2023-09-27T07:48:54,337 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/expected_output 2023-09-27T07:48:54,338 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/expected_output/testfile.annotations.pfam -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/expected_output 2023-09-27T07:48:54,340 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/test-input 2023-09-27T07:48:54,341 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/test-input/testfile.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/test-input 2023-09-27T07:48:54,343 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction 2023-09-27T07:48:54,344 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:48:54,345 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:48:54,347 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/biom-convert-table.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:48:54,349 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/biom-convert-test.job-input.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:48:54,351 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/biom-convert.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:48:54,354 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/biom-convert.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:48:54,357 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/biom-convert_test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:48:54,359 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/empty_tax.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:48:54,362 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/empty_tax.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:48:54,364 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/empty_tax.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:48:54,366 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output 2023-09-27T07:48:54,367 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert 2023-09-27T07:48:54,368 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert/test-mapseq.hdf5 -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert 2023-09-27T07:48:54,372 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert/test-mapseq.json -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert 2023-09-27T07:48:54,375 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert/test-mapseq.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert 2023-09-27T07:48:54,377 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax 2023-09-27T07:48:54,378 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax/empty.html -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax 2023-09-27T07:48:54,385 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax/empty.mseq.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax 2023-09-27T07:48:54,388 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax/empty.txt -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax 2023-09-27T07:48:54,390 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax/empty_json.biom -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax 2023-09-27T07:48:54,392 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:48:54,394 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input/LSU.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:48:54,396 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input/LSU.html -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:48:54,406 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input/LSU.mseq.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:48:54,409 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input/LSU.txt -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:48:54,411 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input/LSU_json.biom -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:48:54,414 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input/test-mapseq.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:48:54,417 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch 2023-09-27T07:48:54,418 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/infernal-cmsearch-v1.1.2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch 2023-09-27T07:48:54,421 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/infernal-cmsearch.test.job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch 2023-09-27T07:48:54,423 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap 2023-09-27T07:48:54,425 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap-v0.02.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap 2023-09-27T07:48:54,427 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap-v0.02.test.job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap 2023-09-27T07:48:54,429 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap 2023-09-27T07:48:54,433 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/expected_output 2023-09-27T07:48:54,434 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/expected_output/1.cmsearch.tblout.deoverlapped -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/expected_output 2023-09-27T07:48:54,438 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/test-input 2023-09-27T07:48:54,440 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/test-input/1.cmsearch.tblout -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/test-input 2023-09-27T07:48:54,447 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/test-input/ribo.claninfo -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/test-input 2023-09-27T07:48:54,449 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/expected_output 2023-09-27T07:48:54,451 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/expected_output/mrum-genome.fa.cmsearch_matches.tbl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/expected_output 2023-09-27T07:48:54,454 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input 2023-09-27T07:48:54,455 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input/mrum-genome.fa -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input 2023-09-27T07:48:54,512 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input/mt-tmRNA.cm -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input 2023-09-27T07:48:54,516 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input/tRNA5.c.cm -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input 2023-09-27T07:48:54,519 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel 2023-09-27T07:48:54,520 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-index.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel 2023-09-27T07:48:54,522 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-sfetch-index-test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel 2023-09-27T07:48:54,524 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-sfetch-index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel 2023-09-27T07:48:54,526 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-sfetch-manyseqs-test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel 2023-09-27T07:48:54,529 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-sfetch-manyseqs.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel 2023-09-27T07:48:54,532 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output 2023-09-27T07:48:54,533 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output/test-cmsearch_matched_seqs_with_coords.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output 2023-09-27T07:48:54,536 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output/test.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output 2023-09-27T07:48:54,538 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output/test.fasta.ssi -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output 2023-09-27T07:48:54,540 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input 2023-09-27T07:48:54,541 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input/matched_seqs_with_coords -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input 2023-09-27T07:48:54,544 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input/test-cmsearch.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input 2023-09-27T07:48:54,546 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input/test.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input 2023-09-27T07:48:54,548 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords 2023-09-27T07:48:54,549 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/awk_tool -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords 2023-09-27T07:48:54,551 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/extract-coords_awk.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords 2023-09-27T07:48:54,554 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/extract-coords_awk.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords 2023-09-27T07:48:54,556 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/expected-output 2023-09-27T07:48:54,557 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/expected-output/matched_seqs_with_coords -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/expected-output 2023-09-27T07:48:54,558 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/test-input 2023-09-27T07:48:54,559 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/test-input/test-cmsearch.txt -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/test-input 2023-09-27T07:48:54,561 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords 2023-09-27T07:48:54,562 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/get_subunits_coords.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords 2023-09-27T07:48:54,565 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/get_subunits_coords.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords 2023-09-27T07:48:54,567 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/get_subunits_coords.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords 2023-09-27T07:48:54,569 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output 2023-09-27T07:48:54,570 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output/5s -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output 2023-09-27T07:48:54,573 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output/LSUs -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output 2023-09-27T07:48:54,575 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output/SSUs -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output 2023-09-27T07:48:54,577 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/test-input 2023-09-27T07:48:54,578 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/test-input/matched_seqs_with_coords -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/test-input 2023-09-27T07:48:54,580 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta 2023-09-27T07:48:54,582 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/get_subunits.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta 2023-09-27T07:48:54,584 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/get_subunits.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta 2023-09-27T07:48:54,587 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/get_subunits.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta 2023-09-27T07:48:54,589 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-input 2023-09-27T07:48:54,590 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-input/test.get_subunits -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-input 2023-09-27T07:48:54,593 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output 2023-09-27T07:48:54,594 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output/5S.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output 2023-09-27T07:48:54,596 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output/LSU.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output 2023-09-27T07:48:54,598 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output/SSU.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output 2023-09-27T07:48:54,601 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output/prefix_LSU_rRNA_bacteria.RF02541.fa -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output 2023-09-27T07:48:54,603 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output/prefix_SSU_rRNA_bacteria.RF00177.fa -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output 2023-09-27T07:48:54,605 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona 2023-09-27T07:48:54,606 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona 2023-09-27T07:48:54,609 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/krona-test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona 2023-09-27T07:48:54,611 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/krona.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona 2023-09-27T07:48:54,613 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/expected-output 2023-09-27T07:48:54,614 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/expected-output/test.html -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/expected-output 2023-09-27T07:48:54,620 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/test-input 2023-09-27T07:48:54,622 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/test-input/test.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/test-input 2023-09-27T07:48:54,625 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq 2023-09-27T07:48:54,626 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq 2023-09-27T07:48:54,629 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq/mapseq-test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq 2023-09-27T07:48:54,631 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq/mapseq.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq 2023-09-27T07:48:54,633 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom 2023-09-27T07:48:54,635 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom 2023-09-27T07:48:54,637 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/mapseq2biom-test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom 2023-09-27T07:48:54,640 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/mapseq2biom.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom 2023-09-27T07:48:54,642 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/mapseq2biom.pl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom 2023-09-27T07:48:54,645 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/expected-output 2023-09-27T07:48:54,646 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/expected-output/test-mapseq.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/expected-output 2023-09-27T07:48:54,649 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/expected-output/test.txt -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/expected-output 2023-09-27T07:48:54,652 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/test-input 2023-09-27T07:48:54,653 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/test-input/test-mapseq -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/test-input 2023-09-27T07:48:54,660 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/test-input/test-otu -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/test-input 2023-09-27T07:48:54,663 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas 2023-09-27T07:48:54,664 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas/pull_ncrnas.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas 2023-09-27T07:48:54,666 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas/pull_ncrnas.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas 2023-09-27T07:48:54,668 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas/pull_ncrnas.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas 2023-09-27T07:48:54,670 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas/expected-output 2023-09-27T07:48:54,671 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas/expected-output/cyano_tmRNA -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas/expected-output 2023-09-27T07:48:54,673 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads 2023-09-27T07:48:54,674 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs 2023-09-27T07:48:54,675 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/clean_motus_output.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs 2023-09-27T07:48:54,677 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/clean_motus_output.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs 2023-09-27T07:48:54,679 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/mOTUs.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs 2023-09-27T07:48:54,681 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/motus-test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs 2023-09-27T07:48:54,683 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/expected-output 2023-09-27T07:48:54,683 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/expected-output/classifications.motus.biom -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/expected-output 2023-09-27T07:48:54,727 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/test-input 2023-09-27T07:48:54,729 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/test-input/unpaired.fq -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/test-input 2023-09-27T07:48:55,081 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/SeqPrep 2023-09-27T07:48:55,082 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/SeqPrep/seqprep.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/SeqPrep 2023-09-27T07:48:55,085 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/SeqPrep/seqprep.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/SeqPrep 2023-09-27T07:48:55,087 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,088 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/LICENSE -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,092 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/Trimmomatic-v0.36-PE.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,095 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/Trimmomatic-v0.36-PE.test.job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,097 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/Trimmomatic-v0.36-SE.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,100 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/Trimmomatic-v0.36-SE.test.job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,102 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/Trimmomatic_PE_test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,105 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/Trimmomatic_SE_test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,107 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic-end_mode.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,110 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic-illumina_clipping.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,113 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic-max_info.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,115 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic-phred.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,118 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic-sliding_window.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,120 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,122 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic_help.txt -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:48:55,125 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output 2023-09-27T07:48:55,126 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output/A1_left_ok.fq.trimmed.fastq -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output 2023-09-27T07:48:55,179 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output/A1_left_ok.fq.trimmed.unpaired.fastq -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output 2023-09-27T07:48:55,181 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output/A1_right_ok.fq.trimmed.fastq -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output 2023-09-27T07:48:55,230 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output/A1_right_ok.fq.trimmed.unpaired.fastq -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output 2023-09-27T07:48:55,232 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks 2023-09-27T07:48:55,234 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/protein_chunker.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks 2023-09-27T07:48:55,236 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/protein_chunker.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks 2023-09-27T07:48:55,239 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/remove_headers.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks 2023-09-27T07:48:55,241 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/remove_headers.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks 2023-09-27T07:48:55,244 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/split_to_chunks.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks 2023-09-27T07:48:55,246 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker 2023-09-27T07:48:55,247 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker 2023-09-27T07:48:55,250 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker/esl-ssplit.pl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker 2023-09-27T07:48:55,253 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker/esl-ssplit.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker 2023-09-27T07:48:55,256 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker/fasta_chunker.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker 2023-09-27T07:48:55,258 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker/fasta_chunker.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker 2023-09-27T07:48:55,261 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/expected-output-fasta_chunker 2023-09-27T07:48:55,262 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/expected-output-fasta_chunker/100_150.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/expected-output-fasta_chunker 2023-09-27T07:48:55,265 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/expected-output-fasta_chunker/1_100.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/expected-output-fasta_chunker 2023-09-27T07:48:55,269 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/test-input 2023-09-27T07:48:55,270 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/test-input/empty.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/test-input 2023-09-27T07:48:55,272 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer 2023-09-27T07:48:55,274 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer 2023-09-27T07:48:55,276 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmsearch.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer 2023-09-27T07:48:55,279 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/db 2023-09-27T07:48:55,280 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/db/db_kofam.hmm.h3i -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/db 2023-09-27T07:48:55,293 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan 2023-09-27T07:48:55,295 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan/chunking-subwf-hmmscan.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan 2023-09-27T07:48:55,297 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan/hmmscan-subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan 2023-09-27T07:48:55,299 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan/hmmscan.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan 2023-09-27T07:48:55,301 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan/hmmscan.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan 2023-09-27T07:48:55,303 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification 2023-09-27T07:48:55,305 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/hmmscan_tab.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification 2023-09-27T07:48:55,307 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/hmmscan_tab_modification.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification 2023-09-27T07:48:55,309 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/hmmscan_tab_modification.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification 2023-09-27T07:48:55,311 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/expected-output 2023-09-27T07:48:55,312 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/expected-output/hmmscan_result.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/expected-output 2023-09-27T07:48:55,315 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/test-input 2023-09-27T07:48:55,316 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/test-input/hmmscan_result.tbl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/test-input 2023-09-27T07:48:55,318 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:48:55,319 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/bedtools.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:48:55,322 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/bedtools.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:48:55,324 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/format-bedfile.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:48:55,326 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/format-bedfile.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:48:55,328 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/its-length-new.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:48:55,331 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/suppress_tax.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:48:55,333 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/suppress_tax_test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:48:55,336 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/bash_scripts 2023-09-27T07:48:55,337 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/bash_scripts/format_bedfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/bash_scripts 2023-09-27T07:48:55,340 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/expected-output 2023-09-27T07:48:55,341 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/expected-output/ITS-maskfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/expected-output 2023-09-27T07:48:55,343 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/expected-output/masked-for-its.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/expected-output 2023-09-27T07:48:55,346 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input 2023-09-27T07:48:55,347 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/SSU-and-LSU -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input 2023-09-27T07:48:55,349 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/test-cmsearch.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input 2023-09-27T07:48:55,351 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/LSU 2023-09-27T07:48:55,352 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/LSU/LSU.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/LSU 2023-09-27T07:48:55,354 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/SSU 2023-09-27T07:48:55,355 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/SSU/SSU.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/SSU 2023-09-27T07:48:55,357 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering 2023-09-27T07:48:55,358 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/qc-filtering-job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering 2023-09-27T07:48:55,360 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/qc-filtering.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering 2023-09-27T07:48:55,362 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/run_quality_filtering.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering 2023-09-27T07:48:55,365 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/expected-output 2023-09-27T07:48:55,366 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/expected-output/stats_summary -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/expected-output 2023-09-27T07:48:55,368 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/expected-output/test_seqs.filtered.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/expected-output 2023-09-27T07:48:55,370 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/test-input 2023-09-27T07:48:55,371 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/test-input/test_seqs.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/test-input 2023-09-27T07:48:55,373 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats 2023-09-27T07:48:55,374 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/Dockerfile -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats 2023-09-27T07:48:55,377 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/MGRAST_base.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats 2023-09-27T07:48:55,379 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/qc-stats-job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats 2023-09-27T07:48:55,382 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/qc-stats.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats 2023-09-27T07:48:55,384 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output 2023-09-27T07:48:55,384 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:48:55,385 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/GC-distribution.out.full -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:48:55,388 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/GC-distribution.out.full_bin -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:48:55,390 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/GC-distribution.out.full_pcbin -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:48:55,392 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/nucleotide-distribution.out.full -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:48:55,394 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/seq-length.out.full -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:48:55,396 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/seq-length.out.full_bin -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:48:55,398 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/seq-length.out.full_pcbin -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:48:55,400 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/test-inputs 2023-09-27T07:48:55,401 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/test-inputs/test.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/test-inputs 2023-09-27T07:48:55,403 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:48:55,404 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries/functional_stats.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:48:55,407 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries/functional_stats.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:48:55,409 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries/functional_stats.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:48:55,411 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries/write_summaries.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:48:55,414 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries/write_summaries.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:48:55,416 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries/write_summaries.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:48:55,418 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,419 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/clean_fasta_headers.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,421 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/concatenate.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,424 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_fasta.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,426 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_fasta.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,428 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_number_lines.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,430 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastp.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,433 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_tab_sep.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,435 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/move.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,437 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/multiple-gunzip.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,439 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/qc-flag.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,441 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/return_directory.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,443 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/return_directory.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,445 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/touch_file.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:48:55,447 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header 2023-09-27T07:48:55,447 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header/add_header -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header 2023-09-27T07:48:55,450 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header/add_header.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header 2023-09-27T07:48:55,452 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header/add_header.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header 2023-09-27T07:48:55,454 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines 2023-09-27T07:48:55,455 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines/count_fastq_exp.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines 2023-09-27T07:48:55,457 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines/count_lines.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines 2023-09-27T07:48:55,459 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines/count_lines.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines 2023-09-27T07:48:55,461 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines/count_lines.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines 2023-09-27T07:48:55,463 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/empty-fasta 2023-09-27T07:48:55,464 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/empty-fasta/empty_fasta.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/empty-fasta 2023-09-27T07:48:55,467 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/empty-fasta/empty_fasta.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/empty-fasta 2023-09-27T07:48:55,469 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/expected_outputs 2023-09-27T07:48:55,469 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/expected_outputs/fasta_chunker 2023-09-27T07:48:55,471 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/expected_outputs/fasta_chunker/test_01_b_test_01_b.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/expected_outputs/fasta_chunker 2023-09-27T07:48:55,473 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/expected_outputs/fasta_chunker/test_02_test_02.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/expected_outputs/fasta_chunker 2023-09-27T07:48:55,475 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker 2023-09-27T07:48:55,476 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker/fasta_chunker.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker 2023-09-27T07:48:55,478 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker/fasta_chunker.test.job.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker 2023-09-27T07:48:55,480 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker/fasta_chunker_test.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker 2023-09-27T07:48:55,482 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta 2023-09-27T07:48:55,483 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta/fastq_to_fasta.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta 2023-09-27T07:48:55,485 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta/fastq_to_fasta.cwltest.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta 2023-09-27T07:48:55,487 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta/fastq_to_fasta.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta 2023-09-27T07:48:55,489 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta/fastq_to_fasta.test.job-input.yaml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta 2023-09-27T07:48:55,491 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/generate_checksum 2023-09-27T07:48:55,492 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/generate_checksum/generate_checksum.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/generate_checksum 2023-09-27T07:48:55,495 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/generate_checksum/generate_checksum.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/generate_checksum 2023-09-27T07:48:55,497 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification 2023-09-27T07:48:55,498 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/hmmscan_tab.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification 2023-09-27T07:48:55,500 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/hmmscan_tab_modification.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification 2023-09-27T07:48:55,502 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/hmmscan_tab_modification.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification 2023-09-27T07:48:55,504 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/expected-output 2023-09-27T07:48:55,505 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/expected-output/hmmscan_result.tsv -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/expected-output 2023-09-27T07:48:55,508 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/test-input 2023-09-27T07:48:55,509 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/test-input/hmmscan_result.tbl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/test-input 2023-09-27T07:48:55,512 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv 2023-09-27T07:48:55,513 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv/make_csv.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv 2023-09-27T07:48:55,515 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv/make_csv.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv 2023-09-27T07:48:55,517 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv/output -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv 2023-09-27T07:48:55,519 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv/test.txt -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv 2023-09-27T07:48:55,521 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/pigz 2023-09-27T07:48:55,522 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/pigz/gzip.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/pigz 2023-09-27T07:48:55,525 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:48:55,526 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/__init__.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:48:55,528 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/chunkFastaResultFileUtil.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:48:55,531 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/chunkTSVFileUtil.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:48:55,533 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/cleaningUtils.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:48:55,536 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/result_chunker.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:48:55,538 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/run_result_file_chunker.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:48:55,541 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/test-inputs 2023-09-27T07:48:55,542 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/test-inputs/test_seqs.fasta -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/test-inputs 2023-09-27T07:48:55,544 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/test-inputs/test_seqs.fq -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/test-inputs 2023-09-27T07:48:55,546 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows 2023-09-27T07:48:55,547 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/amplicon-wf--v.5-cond.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows 2023-09-27T07:48:55,550 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/assembly-wf--v.5-cond.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows 2023-09-27T07:48:55,553 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/raw-reads-wf--v.5-cond.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows 2023-09-27T07:48:55,556 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals 2023-09-27T07:48:55,556 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/README -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals 2023-09-27T07:48:55,559 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/out_json_parser.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals 2023-09-27T07:48:55,561 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/amplicon 2023-09-27T07:48:55,562 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/amplicon/amplicon-1.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/amplicon 2023-09-27T07:48:55,564 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/amplicon/amplicon-2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/amplicon 2023-09-27T07:48:55,567 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/assembly 2023-09-27T07:48:55,568 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/assembly/assembly-1.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/assembly 2023-09-27T07:48:55,570 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/assembly/assembly-2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/assembly 2023-09-27T07:48:55,573 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/raw-reads 2023-09-27T07:48:55,574 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/raw-reads/raw-reads-1.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/raw-reads 2023-09-27T07:48:55,576 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/raw-reads/raw-reads-2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/raw-reads 2023-09-27T07:48:55,579 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/profiling 2023-09-27T07:48:55,580 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/profiling/profiling_parser.py -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/profiling 2023-09-27T07:48:55,582 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/profiling/run_profiling.sh -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/profiling 2023-09-27T07:48:55,585 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:48:55,586 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/chunking-subwf-IPS.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:48:55,588 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/chunking-subwf-hmmsearch.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:48:55,590 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/classify-otu-visualise.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:48:55,593 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/cmsearch-condition.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:48:55,595 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/cmsearch-multimodel-raw-data.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:48:55,598 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/final_chunking.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:48:55,600 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/func_summaries.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:48:55,602 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/other_ncrnas.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:48:55,604 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/rna_prediction-sub-wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:48:55,607 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/seqprep-subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:48:55,609 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon 2023-09-27T07:48:55,610 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon/ITS-wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon 2023-09-27T07:48:55,613 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon/trim_and_reformat_reads.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon 2023-09-27T07:48:55,615 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon/trimming-not-empty-subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon 2023-09-27T07:48:55,617 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:48:55,618 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/CGC-subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:48:55,620 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/change_formats_and_names.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:48:55,623 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/cmsearch-multimodel-assembly.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:48:55,625 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/deal_with_functional_annotation.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:48:55,628 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/func_ann_and_post_processing-subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:48:55,631 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/functional_annotation.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:48:55,634 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/functional_annotation.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:48:55,637 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/kegg_analysis.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:48:55,640 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/kegg_analysis.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:48:55,642 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads 2023-09-27T07:48:55,643 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads/CGC-subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads 2023-09-27T07:48:55,646 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads/func_ann_and_post_proccessing-subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads 2023-09-27T07:48:55,649 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads/functional_annotation_raw.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads 2023-09-27T07:48:55,652 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads/mOTUs-workflow.cwl -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads 2023-09-27T07:48:55,654 creating build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls 2023-09-27T07:48:55,655 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls/amplicon-wf--v.5-cond.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls 2023-09-27T07:48:55,659 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls/assembly-pipeline-v.5.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls 2023-09-27T07:48:55,662 copying janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls/raw-reads--v.5-cond.yml -> build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls 2023-09-27T07:48:55,665 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow 2023-09-27T07:48:55,666 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/README.md -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow 2023-09-27T07:48:55,670 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated 2023-09-27T07:48:55,671 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/kfdrc_production_somatic_variant_cnv_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated 2023-09-27T07:48:55,675 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/samtools_cram2bam_plus_calmd.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated 2023-09-27T07:48:55,678 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config 2023-09-27T07:48:55,679 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config/control_freec.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config 2023-09-27T07:48:55,682 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config/control_freec_R.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config 2023-09-27T07:48:55,685 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config/control_freec_visualize.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config 2023-09-27T07:48:55,688 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config/gen_controlfreec_configfile.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config 2023-09-27T07:48:55,691 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7 2023-09-27T07:48:55,692 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7/control_freec.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7 2023-09-27T07:48:55,696 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7/control_freec_R.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7 2023-09-27T07:48:55,699 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7/control_freec_visualize.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7 2023-09-27T07:48:55,703 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,704 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/build_strelka2_mnp.py -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,708 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/cnv_using_subwf_test.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,712 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/custom_split.py -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,716 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/delme_pbta_temp_vcftomaf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,719 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/delme_tcga_temp_vcftomaf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,724 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/gatk_intervallisttool.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,727 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/gatk_sortvcf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,730 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/gen_germline_controlfreec_config.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,733 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/lancet.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,736 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/output_vcf_pick.py -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,739 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/quick_split_bed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,742 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/samtools_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,746 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/temp_rerun_vcf2maf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,748 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/vardictjava.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:55,751 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:55,753 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/add_strelka2_fields.py -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:55,757 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/consensus_merge.py -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:55,761 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/hotspot.py -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:55,765 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/kf_mskcc_vcf2maf_1.6.21.pl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:55,770 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/sbg_cveto_util.py -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:55,775 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/sbg_multicnv.py -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:55,779 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/sbg_multicnv_methods.py -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:55,783 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/sbg_multicnv_visualisations.py -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:55,786 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:48:55,788 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_cnvkit_sub_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:48:55,790 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_controlfreec_sub_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:48:55,793 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_gatk_cnv_somatic_pair_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:48:55,797 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_lancet_sub_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:48:55,801 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_manta_sub_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:48:55,805 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_mutect2_filter_support_subwf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:48:55,808 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_mutect2_sub_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:48:55,812 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_run_theta2_sub_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:48:55,815 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_strelka2_sub_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:48:55,819 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_vardict_sub_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:48:55,822 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/prepare_reference.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:48:55,826 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,827 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/aa_classifier.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,831 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/add_basename.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,834 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/add_strelka2_fields.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,837 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/amplicon_architect.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,841 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/annotsv.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,844 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/awk_min_seg_length.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,848 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcbio_filter_vardict_somatic.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,851 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcbio_normalize_vcf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,854 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcbio_variant_recall_ensemble.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,857 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcftools_annotate.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,859 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcftools_filter_vcf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,862 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcftools_reheader_vcf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,864 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcftools_strip_ann.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,867 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bedtools_intersect.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,869 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bundle_secondaryfiles.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,872 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bwa_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,875 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/canvas_paired_wes.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,877 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cns_to_aa_bed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,880 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_batch.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,883 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_batch_only.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,886 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_call.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,888 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_export_theta2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,891 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_import_theta2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,894 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvnator.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,896 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/consensus_merge.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,899 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/control-freec-11-6-sbg.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,904 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/control_freec_mini_pileup.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,907 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/expression_flatten_file_list.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,909 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/expression_flatten_list.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,911 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/expression_pickvalue_workaround.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,914 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/expression_run_aa_if_wgs.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,916 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_Mutect2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,919 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_annotateintervals.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,922 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_calculatecontamination.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,924 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_callcopyratiosegments.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,927 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_collectalleliccounts.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,929 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_collectreadcounts.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,932 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_createreadcountpanelofnormals.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,935 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_denoisereadcounts.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,938 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_filter_germline_variant.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,940 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_filtermutectcalls.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,943 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_funcotatesegments.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,946 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_gatherpileupsummaries.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,948 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_getpileupsummaries.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,951 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_indexfeaturefile.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,953 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_intervallisttool.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,956 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_learnorientationbias.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,958 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_mergemutectstats.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,960 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_mergevcfs.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,963 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_modelsegments.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,966 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_plotdenoisedcopyratios.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,969 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_plotmodeledsegments.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,971 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_preprocessintervals.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,974 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_selectvariants.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,976 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_sortvcf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,979 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_variant_filter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,981 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/generic_rename_outputs.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,984 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/hotspots_annotation.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,986 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/kf_mskcc_vcf2maf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,989 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/lancet.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,991 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/lumpy-sv_germline.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,994 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/lumpy-sv_somatic.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,996 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/manta.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:55,999 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/mode_defaults.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,001 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/mode_list_selector.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,004 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/mode_selector.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,006 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/normalize_vcf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,009 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/picard_createsequencedictionary.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,011 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/prep_mnp_variants.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,014 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/prepare_aa.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,016 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/preprocess_lancet_intervals.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,019 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/python_vardict_interval_split.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,021 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/samtools_calmd.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,023 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/samtools_cram2bam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,026 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/samtools_faidx.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,028 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/samtools_reheader_bam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,031 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/sb_multicnv_1_0_0.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,034 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/sb_multicnv_prepare_files_for_scatter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,036 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/sb_multicnv_rename_files.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,039 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/seurat.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,042 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/smoove_lumpy.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,044 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/snpEff_annotate.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,047 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/speedseq_sv_annotate.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,050 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/strelka2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,053 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/tabix_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,056 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/tar.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,058 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/theta2_purity.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,060 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/ubuntu_ratio2seg.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,063 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/ubuntu_rename_outputs.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,065 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/untar_gzip.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,068 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/vardictjava.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,070 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/variant_effect_predictor_105.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:56,073 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,074 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc-somatic-variant-workflow.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,078 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_annot_vcf_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,081 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_consensus_calling.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,084 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_gatk_create_cnv_pon_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,087 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_amplicon_architect.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,090 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_cnvkit_theta2_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,093 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_cnvkit_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,096 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_controlfreec_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,099 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_lancet_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,102 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_manta_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,104 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_mutect2_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,107 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_strelka2_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,110 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_theta2_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,113 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_vardict_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,116 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/sb_multicnv_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:56,119 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated 2023-09-27T07:48:56,121 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/config -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated 2023-09-27T07:48:56,124 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/main.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated 2023-09-27T07:48:56,127 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,128 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/FGS.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,131 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/QC_FLAG.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,133 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/add_crossmapped_to_resmapped.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,135 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/add_domain_positions.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,138 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/align_avg_structs_pairwise.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,140 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/antismash_gff.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,143 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/antismash_summary.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,145 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_averaged_structures.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,148 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_averaged_unp_domains.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,151 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_chopped_structs_unp_domains.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,153 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_chopped_structures_unp_domains.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,155 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/bam_index.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,158 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/calc_chunking_number.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,160 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/carveme.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,163 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/carveme_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,165 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/cat.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,167 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/cat_models.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,169 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/check_alignment_scores.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,172 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/check_threshold_step.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,174 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/check_value.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,176 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chinking_SC_fasta_nucleotide.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,179 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chinking_fasta_nucleotide.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,181 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chinking_fasta_proteins.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,184 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chop_structs.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,186 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chunking_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,188 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chunking_tsv.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,191 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/classifications_to_otu_counts.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,193 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/clean_classification.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,196 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/clean_fasta_headers.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,198 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/clean_headers.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,200 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/cmsearch.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,203 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/collect_lost_instances.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,206 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/combine.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,208 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/combine_ips.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,210 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/combine_trimmed.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,213 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compare_instances_CATH_Pfam.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,215 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,219 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress_carveme.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,222 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress_mapseq.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,224 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress_prodigal.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,227 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compression.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,229 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compression_func_ann.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,232 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/conversion.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,234 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/convert_trimmed_reads_to_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,236 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/copy_avg_dom.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,239 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_ITS_seqs.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,241 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_cds.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,244 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_lines_mapseq.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,246 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_lsu_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,248 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_masked_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,251 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_overlapped_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,253 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_processed_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,255 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,258 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_reads_after_filtering.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,260 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_ssu_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,263 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_submitted_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,265 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_submitted_reads_single.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,268 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/counts_to_hdf5.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,270 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/counts_to_json.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,273 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/create_csv_gp.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,275 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/create_csv_kp.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,278 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/create_new_parameters.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,280 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/crossmapping_CATH2Pfam.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,283 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/crossmapping_Pfam2CATH.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,285 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/diamond_run.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,288 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/eggnog_annotation.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,290 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/eggnog_homology_searches.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,293 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/expressiontool_bam_index.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,295 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_coords.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,297 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_sequences.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,300 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_subunits.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,302 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_subunits_coords.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,305 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fasta_index.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,307 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fastqc.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,310 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fastqc_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,312 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_cath_structures.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,315 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_contigs_antismash.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,317 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_paired.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,319 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_pfam_structures.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,322 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fix_embl_and_gbk.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,325 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fix_geneclusters_txt.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,328 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/folder_compression.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,331 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/format_core_list.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,334 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/functional_stats.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,337 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gather_domain_like.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,339 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gather_failed_domains.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,341 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gemstats.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,344 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/genome_properties.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,346 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/get_coords.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,348 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/get_family_ids.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,351 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/get_ncrnas.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,353 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gff.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,356 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/go_summary.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,358 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,360 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_LSU.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,363 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_SSU.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,365 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_files.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,367 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_masked_ITS.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,370 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzipped_embl.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,372 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzipped_gbk.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,375 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hashsum.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,377 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hashsum_paired.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,379 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hashsum_single.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,381 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/header_addition.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,384 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hmmsearch.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,386 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/index_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,388 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/interproscan.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,391 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/join.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,393 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/kegg_pathways.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,396 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/kofamscan.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,398 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/length_filter.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,401 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/make_tab_sep.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,403 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/mapseq.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,406 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/mask_for_ITS.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,408 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/memote_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,411 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/memote_report_snapshot.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,414 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/memote_run.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,416 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/motus_classification.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,419 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_antismash_summary_to_pathways_systems_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,421 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_to_functional_annotation_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,423 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_to_pathways_systems_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,426 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_to_seq_cat_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,428 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/ngtax.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,431 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/ngtax_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,433 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/ngtax_to_tsv_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,436 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/no_tax_file_flag.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,438 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/overlap_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,441 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/pairwise_align_avg_structs.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,444 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/parsing_hmmscan.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,447 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/per_dom_instance.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,451 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/per_unp_dom_instance.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,453 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/pfam.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,456 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/phyloseq_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,458 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/picrust2.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,461 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/picrust_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,463 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/pilon.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,466 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/post_processing.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,468 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/prodigal.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,471 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/prodigal_files_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,474 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/qc_stats.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,477 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/readmapping_pilon.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,480 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/reads_to_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,483 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/reformat_coords.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,486 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/remove_overlaps.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,488 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/rename_contigs.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,490 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/rename_geneclusters.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,493 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/rename_ncrnas.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,495 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/resmapping_for_CATH_PDB2UP.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,498 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/resmapping_for_Pfam_UP2PDB.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,500 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_antismash_in_folder.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,503 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_its_dir.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,505 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_output_dir.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,508 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_seq_dir.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,510 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_tax_dir.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,513 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_antismash.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,515 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_concatenate_deoverlapped_matches.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,518 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_concatenate_matches.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,524 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_quality_control_filtering.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,529 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/sam_to_sorted_bam.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,532 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/smetana.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,534 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/sorting.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,537 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/split_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,539 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/split_seqs.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,542 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/suppress_tax.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,544 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/tab_modification.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,547 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/tohdt.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,549 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_empty_fasta.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,552 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_file_flag.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,555 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_no_antismash_flag.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,558 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_no_cds_flag.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,562 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/trim_quality_control.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,564 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_embl.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,566 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_gbk.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,569 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_geneclusters_txt.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,571 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_seed_orthologs.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,574 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unzip.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,576 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unzip_merged_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,578 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unzip_single_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,581 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/vcf_compress.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,583 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/visualize_otu_counts.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,586 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/write_summaries.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:56,588 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,589 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/ITS.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,592 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/after_qc.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,597 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/antismash.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,600 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/avg_unp_domains.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,602 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/before_qc.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,605 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cath_domain_instances.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,608 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cgc.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,610 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/change_formats_and_names.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,612 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_for_CATH2Pfam.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,615 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_for_Pfam2CATH.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,617 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_for_core.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,620 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_from_list.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,622 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chunking.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,626 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chunking_final.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,628 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/classify_LSUs.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,631 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/classify_SSUs.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,634 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cmsearch_assembly.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,637 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cmsearch_raw_data.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,640 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/combined_gene_caller.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,643 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/diamond.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,645 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/eggnog.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,652 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/filtering.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,654 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/find_ribosomal_ncRNAs.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,657 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/folder_functional_annotation.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,660 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/functional_annotation.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,662 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/functional_annotation_and_post_processing.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,665 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/motus_taxonomy.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,667 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/no_antismash_subwf.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,670 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/other_ncrnas.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,672 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/overlap_reads.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,675 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/pathways.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,677 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/pfam_domain_instances.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,680 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/post_processing_uniref90.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,682 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/resmapping_cath_structs.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,685 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/resmapping_pfam_structs.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,687 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/rna_prediction.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,691 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_IPS.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,693 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_antismash.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,696 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_hmmer.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,698 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_itsonedb.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,701 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_unite.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,703 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/trimming.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,706 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/unmapped_from_cath.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,708 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/unmapped_from_pfam.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,711 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/write_summaries.nf -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:56,714 creating build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,715 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/cnvkit_single_sample_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,719 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/control-freec-germline.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,721 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_cnv_caller_wes_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,724 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_cnvkit_batch_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,727 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_cnvkit_plus_theta2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,730 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_combined_somatic_wgs_cnv_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,733 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_controlfreec_cnv.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,736 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_lancet_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,739 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_mutect2_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,742 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_production_WES_somatic_variant_cnv_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,745 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_production_WGS_somatic_variant_cnv.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,748 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_somatic_WES_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,751 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_somatic_caller_workflow.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,754 copying janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_vardict_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:56,757 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock 2023-09-27T07:48:56,757 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq 2023-09-27T07:48:56,759 copying janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/.gitkeep -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq 2023-09-27T07:48:56,761 copying janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/featurecounts.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq 2023-09-27T07:48:56,763 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/kallisto 2023-09-27T07:48:56,765 copying janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/kallisto/kallisto_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/kallisto 2023-09-27T07:48:56,767 copying janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/kallisto/kallisto_quant.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/kallisto 2023-09-27T07:48:56,770 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/star 2023-09-27T07:48:56,772 copying janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/star/star_align.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/star 2023-09-27T07:48:56,775 copying janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/star/star_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/star 2023-09-27T07:48:56,777 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/aragorn 2023-09-27T07:48:56,778 copying janis_core/tests/data/cwl/workflows/m-unlock/aragorn/aragorn.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/aragorn 2023-09-27T07:48:56,781 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:48:56,782 copying janis_core/tests/data/cwl/workflows/m-unlock/bash/compress.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:48:56,785 copying janis_core/tests/data/cwl/workflows/m-unlock/bash/compress_directory.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:48:56,787 copying janis_core/tests/data/cwl/workflows/m-unlock/bash/concatenate.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:48:56,789 copying janis_core/tests/data/cwl/workflows/m-unlock/bash/decompress.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:48:56,791 copying janis_core/tests/data/cwl/workflows/m-unlock/bash/grep_count.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:48:56,794 copying janis_core/tests/data/cwl/workflows/m-unlock/bash/pigz.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:48:56,796 copying janis_core/tests/data/cwl/workflows/m-unlock/bash/rename.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:48:56,798 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bbmap 2023-09-27T07:48:56,799 copying janis_core/tests/data/cwl/workflows/m-unlock/bbmap/bbduk_filter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bbmap 2023-09-27T07:48:56,801 copying janis_core/tests/data/cwl/workflows/m-unlock/bbmap/bbduk_rrna-filter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bbmap 2023-09-27T07:48:56,803 copying janis_core/tests/data/cwl/workflows/m-unlock/bbmap/bbmap.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bbmap 2023-09-27T07:48:56,806 copying janis_core/tests/data/cwl/workflows/m-unlock/bbmap/bbmap_filter-reads.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bbmap 2023-09-27T07:48:56,808 copying janis_core/tests/data/cwl/workflows/m-unlock/bbmap/prepare_fasta_db.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bbmap 2023-09-27T07:48:56,810 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bowtie2 2023-09-27T07:48:56,811 copying janis_core/tests/data/cwl/workflows/m-unlock/bowtie2/bowtie2_align.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bowtie2 2023-09-27T07:48:56,814 copying janis_core/tests/data/cwl/workflows/m-unlock/bowtie2/bowtie2_align_simple.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bowtie2 2023-09-27T07:48:56,817 copying janis_core/tests/data/cwl/workflows/m-unlock/bowtie2/bowtie2_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bowtie2 2023-09-27T07:48:56,819 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/busco 2023-09-27T07:48:56,820 copying janis_core/tests/data/cwl/workflows/m-unlock/busco/busco.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/busco 2023-09-27T07:48:56,822 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/carveme 2023-09-27T07:48:56,823 copying janis_core/tests/data/cwl/workflows/m-unlock/carveme/GEMstats.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/carveme 2023-09-27T07:48:56,826 copying janis_core/tests/data/cwl/workflows/m-unlock/carveme/carveme.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/carveme 2023-09-27T07:48:56,829 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/checkm 2023-09-27T07:48:56,829 copying janis_core/tests/data/cwl/workflows/m-unlock/checkm/checkm_lineagewf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/checkm 2023-09-27T07:48:56,832 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/clustalo 2023-09-27T07:48:56,833 copying janis_core/tests/data/cwl/workflows/m-unlock/clustalo/clustalo.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/clustalo 2023-09-27T07:48:56,835 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/das_tool 2023-09-27T07:48:56,836 copying janis_core/tests/data/cwl/workflows/m-unlock/das_tool/das_tool.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/das_tool 2023-09-27T07:48:56,838 copying janis_core/tests/data/cwl/workflows/m-unlock/das_tool/fasta_to_contig2bin.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/das_tool 2023-09-27T07:48:56,841 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/diamond 2023-09-27T07:48:56,842 copying janis_core/tests/data/cwl/workflows/m-unlock/diamond/diamond.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/diamond 2023-09-27T07:48:56,846 copying janis_core/tests/data/cwl/workflows/m-unlock/diamond/view.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/diamond 2023-09-27T07:48:56,848 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/ena 2023-09-27T07:48:56,849 copying janis_core/tests/data/cwl/workflows/m-unlock/ena/ena_wget.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/ena 2023-09-27T07:48:56,851 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/eukrep 2023-09-27T07:48:56,853 copying janis_core/tests/data/cwl/workflows/m-unlock/eukrep/eukrep.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/eukrep 2023-09-27T07:48:56,855 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:48:56,856 copying janis_core/tests/data/cwl/workflows/m-unlock/expressions/array_to_file.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:48:56,858 copying janis_core/tests/data/cwl/workflows/m-unlock/expressions/files_to_folder.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:48:56,860 copying janis_core/tests/data/cwl/workflows/m-unlock/expressions/folder_file_regex.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:48:56,863 copying janis_core/tests/data/cwl/workflows/m-unlock/expressions/folder_to_files.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:48:56,865 copying janis_core/tests/data/cwl/workflows/m-unlock/expressions/merge_dir_arrays.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:48:56,867 copying janis_core/tests/data/cwl/workflows/m-unlock/expressions/merge_file_arrays.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:48:56,869 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/fastp 2023-09-27T07:48:56,870 copying janis_core/tests/data/cwl/workflows/m-unlock/fastp/fastp.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/fastp 2023-09-27T07:48:56,872 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/fastq 2023-09-27T07:48:56,873 copying janis_core/tests/data/cwl/workflows/m-unlock/fastq/fastq_to_fasta.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/fastq 2023-09-27T07:48:56,875 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/fastqc 2023-09-27T07:48:56,876 copying janis_core/tests/data/cwl/workflows/m-unlock/fastqc/fastqc.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/fastqc 2023-09-27T07:48:56,878 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/filtlong 2023-09-27T07:48:56,879 copying janis_core/tests/data/cwl/workflows/m-unlock/filtlong/filtlong.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/filtlong 2023-09-27T07:48:56,881 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/flye 2023-09-27T07:48:56,882 copying janis_core/tests/data/cwl/workflows/m-unlock/flye/flye.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/flye 2023-09-27T07:48:56,885 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/gtdbtk 2023-09-27T07:48:56,886 copying janis_core/tests/data/cwl/workflows/m-unlock/gtdbtk/gtdbtk_classify_wf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/gtdbtk 2023-09-27T07:48:56,888 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/gunc 2023-09-27T07:48:56,889 copying janis_core/tests/data/cwl/workflows/m-unlock/gunc/gunc.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/gunc 2023-09-27T07:48:56,891 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/guppy 2023-09-27T07:48:56,892 copying janis_core/tests/data/cwl/workflows/m-unlock/guppy/guppy.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/guppy 2023-09-27T07:48:56,894 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/humann 2023-09-27T07:48:56,895 copying janis_core/tests/data/cwl/workflows/m-unlock/humann/humann.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/humann 2023-09-27T07:48:56,897 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/irods 2023-09-27T07:48:56,899 copying janis_core/tests/data/cwl/workflows/m-unlock/irods/irods_hdt.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/irods 2023-09-27T07:48:56,901 copying janis_core/tests/data/cwl/workflows/m-unlock/irods/irods_manager.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/irods 2023-09-27T07:48:56,903 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/kraken2 2023-09-27T07:48:56,904 copying janis_core/tests/data/cwl/workflows/m-unlock/kraken2/kraken2-build.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/kraken2 2023-09-27T07:48:56,906 copying janis_core/tests/data/cwl/workflows/m-unlock/kraken2/kraken2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/kraken2 2023-09-27T07:48:56,908 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/krona 2023-09-27T07:48:56,909 copying janis_core/tests/data/cwl/workflows/m-unlock/krona/krona.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/krona 2023-09-27T07:48:56,911 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/longqc 2023-09-27T07:48:56,912 copying janis_core/tests/data/cwl/workflows/m-unlock/longqc/longqc.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/longqc 2023-09-27T07:48:56,914 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/maxbin2 2023-09-27T07:48:56,915 copying janis_core/tests/data/cwl/workflows/m-unlock/maxbin2/maxbin2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/maxbin2 2023-09-27T07:48:56,917 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/medaka 2023-09-27T07:48:56,918 copying janis_core/tests/data/cwl/workflows/m-unlock/medaka/medaka.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/medaka 2023-09-27T07:48:56,920 copying janis_core/tests/data/cwl/workflows/m-unlock/medaka/medaka_py.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/medaka 2023-09-27T07:48:56,923 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/memote 2023-09-27T07:48:56,924 copying janis_core/tests/data/cwl/workflows/m-unlock/memote/memote.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/memote 2023-09-27T07:48:56,926 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/merge 2023-09-27T07:48:56,926 copying janis_core/tests/data/cwl/workflows/m-unlock/merge/merge.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/merge 2023-09-27T07:48:56,929 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metabat2 2023-09-27T07:48:56,930 copying janis_core/tests/data/cwl/workflows/m-unlock/metabat2/aggregateBinDepths.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metabat2 2023-09-27T07:48:56,932 copying janis_core/tests/data/cwl/workflows/m-unlock/metabat2/metabat2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metabat2 2023-09-27T07:48:56,934 copying janis_core/tests/data/cwl/workflows/m-unlock/metabat2/metabatContigDepths.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metabat2 2023-09-27T07:48:56,936 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metagenomics 2023-09-27T07:48:56,937 copying janis_core/tests/data/cwl/workflows/m-unlock/metagenomics/assembly_bins_readstats.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metagenomics 2023-09-27T07:48:56,940 copying janis_core/tests/data/cwl/workflows/m-unlock/metagenomics/bins_summary.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metagenomics 2023-09-27T07:48:56,942 copying janis_core/tests/data/cwl/workflows/m-unlock/metagenomics/get_unbinned_contigs.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metagenomics 2023-09-27T07:48:56,944 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/minimap2 2023-09-27T07:48:56,945 copying janis_core/tests/data/cwl/workflows/m-unlock/minimap2/minimap2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/minimap2 2023-09-27T07:48:56,947 copying janis_core/tests/data/cwl/workflows/m-unlock/minimap2/minimap2_to_fastq.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/minimap2 2023-09-27T07:48:56,950 copying janis_core/tests/data/cwl/workflows/m-unlock/minimap2/minimap2_to_sorted-bam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/minimap2 2023-09-27T07:48:56,952 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/minionqc 2023-09-27T07:48:56,953 copying janis_core/tests/data/cwl/workflows/m-unlock/minionqc/minionqc.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/minionqc 2023-09-27T07:48:56,955 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/multiqc 2023-09-27T07:48:56,956 copying janis_core/tests/data/cwl/workflows/m-unlock/multiqc/multiqc.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/multiqc 2023-09-27T07:48:56,958 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/nanoqc 2023-09-27T07:48:56,959 copying janis_core/tests/data/cwl/workflows/m-unlock/nanoqc/nanoqc.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/nanoqc 2023-09-27T07:48:56,961 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/ngtax 2023-09-27T07:48:56,962 copying janis_core/tests/data/cwl/workflows/m-unlock/ngtax/ngtax.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/ngtax 2023-09-27T07:48:56,964 copying janis_core/tests/data/cwl/workflows/m-unlock/ngtax/ngtax_demultiplexing.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/ngtax 2023-09-27T07:48:56,966 copying janis_core/tests/data/cwl/workflows/m-unlock/ngtax/ngtax_to_biom.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/ngtax 2023-09-27T07:48:56,968 copying janis_core/tests/data/cwl/workflows/m-unlock/ngtax/ngtax_to_tsv-fasta.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/ngtax 2023-09-27T07:48:56,970 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:56,971 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_RNAseq_NonSpliced_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:56,976 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_RNAseq_Spliced_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:56,980 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_RNAseq_kallisto_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:56,985 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_demultiplexing_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:56,987 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_ena_annotation_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:56,989 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_genomesync_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:56,992 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_illumina_assembly_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:56,997 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_illumina_quality_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,002 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_indexbuilder_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,005 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_longread_quality_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,009 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_GEM_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,013 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_assembly_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,026 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_binning_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,031 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,033 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_read_annotation_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,038 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_microbial_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,041 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_mock_ngtax_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,044 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_nanopore_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,046 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_ngtax_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,050 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_ngtax_picrust2_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,054 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_pilon_mapping_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,057 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_prepare_fasta_db_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,060 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_samsa2_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,064 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_sapp_microbes_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,067 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_sapp_others_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,070 copying janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_toHDT_compression_packed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:48:57,073 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/picrust2 2023-09-27T07:48:57,074 copying janis_core/tests/data/cwl/workflows/m-unlock/picrust2/picrust2_pipeline.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/picrust2 2023-09-27T07:48:57,077 copying janis_core/tests/data/cwl/workflows/m-unlock/picrust2/picrust_to_biom.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/picrust2 2023-09-27T07:48:57,079 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/pilon 2023-09-27T07:48:57,080 copying janis_core/tests/data/cwl/workflows/m-unlock/pilon/pilon.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/pilon 2023-09-27T07:48:57,082 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/prodigal 2023-09-27T07:48:57,083 copying janis_core/tests/data/cwl/workflows/m-unlock/prodigal/prodigal.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/prodigal 2023-09-27T07:48:57,086 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/pycoqc 2023-09-27T07:48:57,087 copying janis_core/tests/data/cwl/workflows/m-unlock/pycoqc/pycoqc.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/pycoqc 2023-09-27T07:48:57,089 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/quast 2023-09-27T07:48:57,090 copying janis_core/tests/data/cwl/workflows/m-unlock/quast/metaquast.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/quast 2023-09-27T07:48:57,093 copying janis_core/tests/data/cwl/workflows/m-unlock/quast/quast.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/quast 2023-09-27T07:48:57,095 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/resfinder 2023-09-27T07:48:57,096 copying janis_core/tests/data/cwl/workflows/m-unlock/resfinder/resfinder.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/resfinder 2023-09-27T07:48:57,098 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samsa2 2023-09-27T07:48:57,100 copying janis_core/tests/data/cwl/workflows/m-unlock/samsa2/convert.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samsa2 2023-09-27T07:48:57,102 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:48:57,103 copying janis_core/tests/data/cwl/workflows/m-unlock/samtools/expression_bam_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:48:57,105 copying janis_core/tests/data/cwl/workflows/m-unlock/samtools/merge-sorted-bam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:48:57,107 copying janis_core/tests/data/cwl/workflows/m-unlock/samtools/sam_to_fastq_PE.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:48:57,110 copying janis_core/tests/data/cwl/workflows/m-unlock/samtools/sam_to_fastq_SE.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:48:57,112 copying janis_core/tests/data/cwl/workflows/m-unlock/samtools/sam_to_sorted-bam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:48:57,114 copying janis_core/tests/data/cwl/workflows/m-unlock/samtools/sam_to_unmapped_fastq_SE.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:48:57,116 copying janis_core/tests/data/cwl/workflows/m-unlock/samtools/samtools_flagstat.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:48:57,119 copying janis_core/tests/data/cwl/workflows/m-unlock/samtools/samtools_idxstats.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:48:57,121 copying janis_core/tests/data/cwl/workflows/m-unlock/samtools/samtools_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:48:57,123 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:48:57,124 copying janis_core/tests/data/cwl/workflows/m-unlock/sapp/conversion.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:48:57,127 copying janis_core/tests/data/cwl/workflows/m-unlock/sapp/conversion_rdf2fasta.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:48:57,129 copying janis_core/tests/data/cwl/workflows/m-unlock/sapp/conversion_rdf2gtf.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:48:57,132 copying janis_core/tests/data/cwl/workflows/m-unlock/sapp/crt.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:48:57,135 copying janis_core/tests/data/cwl/workflows/m-unlock/sapp/infernal.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:48:57,138 copying janis_core/tests/data/cwl/workflows/m-unlock/sapp/interproscan.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:48:57,141 copying janis_core/tests/data/cwl/workflows/m-unlock/sapp/kofamscan.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:48:57,144 copying janis_core/tests/data/cwl/workflows/m-unlock/sapp/prodigal.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:48:57,146 copying janis_core/tests/data/cwl/workflows/m-unlock/sapp/toHDT.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:48:57,149 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/semibin 2023-09-27T07:48:57,151 copying janis_core/tests/data/cwl/workflows/m-unlock/semibin/semibin_rename_bins.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/semibin 2023-09-27T07:48:57,154 copying janis_core/tests/data/cwl/workflows/m-unlock/semibin/semibin_single_easy_bin.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/semibin 2023-09-27T07:48:57,158 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/smetana 2023-09-27T07:48:57,160 copying janis_core/tests/data/cwl/workflows/m-unlock/smetana/smetana.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/smetana 2023-09-27T07:48:57,164 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/spades 2023-09-27T07:48:57,166 copying janis_core/tests/data/cwl/workflows/m-unlock/spades/spades.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/spades 2023-09-27T07:48:57,169 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/stats 2023-09-27T07:48:57,170 copying janis_core/tests/data/cwl/workflows/m-unlock/stats/raw_n50.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/stats 2023-09-27T07:48:57,173 copying janis_core/tests/data/cwl/workflows/m-unlock/stats/seqinfo.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/stats 2023-09-27T07:48:57,176 creating build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:48:57,177 copying janis_core/tests/data/cwl/workflows/m-unlock/workflows/demultiplexing.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:48:57,180 copying janis_core/tests/data/cwl/workflows/m-unlock/workflows/metagenomics_GEM.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:48:57,184 copying janis_core/tests/data/cwl/workflows/m-unlock/workflows/mock_ngtax.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:48:57,187 copying janis_core/tests/data/cwl/workflows/m-unlock/workflows/ngtax.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:48:57,190 copying janis_core/tests/data/cwl/workflows/m-unlock/workflows/ngtax_picrust2.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:48:57,194 copying janis_core/tests/data/cwl/workflows/m-unlock/workflows/pilon_mapping.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:48:57,197 copying janis_core/tests/data/cwl/workflows/m-unlock/workflows/sapp_microbes.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:48:57,201 copying janis_core/tests/data/cwl/workflows/m-unlock/workflows/toHDT_compression.cwl -> build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:48:57,204 creating build/lib/janis_core/tests/data/cwl/workflows/structuralvariants 2023-09-27T07:48:57,206 copying janis_core/tests/data/cwl/workflows/structuralvariants/workflow.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants 2023-09-27T07:48:57,210 copying janis_core/tests/data/cwl/workflows/structuralvariants/workflow.yaml -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants 2023-09-27T07:48:57,213 copying janis_core/tests/data/cwl/workflows/structuralvariants/workflow_idxs.yaml -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants 2023-09-27T07:48:57,216 creating build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,217 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/batch_parser.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,220 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bedops_union.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,223 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bgzip.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,226 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bundle_secondaryfiles.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,229 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bwa_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,232 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bwa_mem_paired.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,235 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bwa_mem_unpaired.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,237 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/codex.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,239 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/codex_filter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,242 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/collapse.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,244 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/exome_depth.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,246 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/exome_depth_filter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,249 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/fastp.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,252 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/fastqc.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,254 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/gridss.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,256 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/gridss_filter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,259 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/gunzip.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,261 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/manta.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,263 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/manta_filter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,265 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/merge_all.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,267 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/picard_markduplicates.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,270 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_faidx.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,272 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,274 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_merge.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,276 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_sort.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,278 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_view.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,280 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_view_sam2bam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,282 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/structural_variants.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,284 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/svtools.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,287 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/tabix.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:57,290 creating build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,291 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/bam_filtering.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,294 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/bwa_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,296 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/bwa_mem.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,299 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/cnv_codex.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,301 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/cnv_exome_depth.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,303 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/cnv_gridss.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,306 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/cnv_manta.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,308 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/final_filtering.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,310 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/indexing_bed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,312 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/picard_markduplicates.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,314 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/samtools_sort.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,317 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/samtools_view_sam2bam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,319 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/trimmed_fastq.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:57,321 creating build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_workflow 2023-09-27T07:48:57,322 copying janis_core/tests/data/cwl/workflows/structuralvariants/abstract_workflow/abstract_workflow.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_workflow 2023-09-27T07:48:57,325 creating build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,326 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/bam_filtering.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,328 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/bwa_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,330 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/bwa_mem.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,333 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/cnv_codex.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,335 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/cnv_exome_depth.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,337 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/cnv_gridss.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,339 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/cnv_manta.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,341 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/final_filtering.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,344 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/indexing_bed.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,346 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/indexing_bed.yaml -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,348 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/picard_markduplicates.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,350 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/samtools_sort.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,353 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/samtools_view_sam2bam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,355 copying janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/trimmed_fastq.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:57,357 creating build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,358 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/batch_parser.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,360 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/bedops_union.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,363 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/bgzip.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,365 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/bundle_secondaryfiles.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,367 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,369 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_index_grace.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,372 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_mem_paired.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,375 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_mem_paired_grace.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,378 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_mem_unpaired.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,380 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_mem_unpaired_grace.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,382 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/codex.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,384 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/codex_filter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,387 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/collapse.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,389 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/exome_depth.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,391 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/exome_depth_filter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,394 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/fastp.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,396 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/fastqc.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,398 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/gridss.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,400 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/gridss_filter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,402 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/gunzip.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,404 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/manta.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,407 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/manta_filter.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,409 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/merge_all.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,411 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/picard_markduplicates.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,413 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_faidx.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,415 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_index.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,418 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_merge.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,419 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_sort.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,422 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_view.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,424 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_view_sam2bam.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,426 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/structural_variants.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,428 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/svtools.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,430 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/tabix.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,432 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/tools_list.txt -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,434 copying janis_core/tests/data/cwl/workflows/structuralvariants/tools/unicycler.cwl -> build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:57,437 creating build/lib/janis_core/tests/data/cwl/workflows/subworkflow_test 2023-09-27T07:48:57,438 copying janis_core/tests/data/cwl/workflows/subworkflow_test/basic.cwl -> build/lib/janis_core/tests/data/cwl/workflows/subworkflow_test 2023-09-27T07:48:57,440 copying janis_core/tests/data/cwl/workflows/subworkflow_test/main.cwl -> build/lib/janis_core/tests/data/cwl/workflows/subworkflow_test 2023-09-27T07:48:57,442 copying janis_core/tests/data/cwl/workflows/subworkflow_test/mandatory_input_types.cwl -> build/lib/janis_core/tests/data/cwl/workflows/subworkflow_test 2023-09-27T07:48:57,444 copying janis_core/tests/data/cwl/workflows/subworkflow_test/optional_input_types.cwl -> build/lib/janis_core/tests/data/cwl/workflows/subworkflow_test 2023-09-27T07:48:57,446 copying janis_core/tests/data/cwl/workflows/subworkflow_test/subworkflow.cwl -> build/lib/janis_core/tests/data/cwl/workflows/subworkflow_test 2023-09-27T07:48:57,448 creating build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,449 copying janis_core/tests/data/galaxy/annotate-my-ids-wf.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,452 copying janis_core/tests/data/galaxy/cutadapt_wf.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,454 copying janis_core/tests/data/galaxy/fastqc_wf.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,457 copying janis_core/tests/data/galaxy/goseq_wf.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,459 copying janis_core/tests/data/galaxy/hisat2_wf.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,462 copying janis_core/tests/data/galaxy/limma_voom_wf.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,465 copying janis_core/tests/data/galaxy/nanoplot_wf.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,467 copying janis_core/tests/data/galaxy/rna_seq_counts_to_genes.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,470 copying janis_core/tests/data/galaxy/rna_seq_genes_to_pathways.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,473 copying janis_core/tests/data/galaxy/rna_seq_reads_to_counts.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,476 copying janis_core/tests/data/galaxy/unicycler_assembly.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,479 copying janis_core/tests/data/galaxy/wf_abricate.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,481 copying janis_core/tests/data/galaxy/wf_featurecounts.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,483 copying janis_core/tests/data/galaxy/wf_mark_duplicates.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,485 copying janis_core/tests/data/galaxy/wf_samtools_idxstats.ga -> build/lib/janis_core/tests/data/galaxy 2023-09-27T07:48:57,487 creating build/lib/janis_core/tests/data/galaxy/abricate 2023-09-27T07:48:57,489 copying janis_core/tests/data/galaxy/abricate/.shed.yml -> build/lib/janis_core/tests/data/galaxy/abricate 2023-09-27T07:48:57,492 copying janis_core/tests/data/galaxy/abricate/abricate.xml -> build/lib/janis_core/tests/data/galaxy/abricate 2023-09-27T07:48:57,495 copying janis_core/tests/data/galaxy/abricate/abricate_list.xml -> build/lib/janis_core/tests/data/galaxy/abricate 2023-09-27T07:48:57,497 copying janis_core/tests/data/galaxy/abricate/abricate_summary.xml -> build/lib/janis_core/tests/data/galaxy/abricate 2023-09-27T07:48:57,500 copying janis_core/tests/data/galaxy/abricate/macros.xml -> build/lib/janis_core/tests/data/galaxy/abricate 2023-09-27T07:48:57,502 creating build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,503 copying janis_core/tests/data/galaxy/abricate/test-data/Acetobacter.fna -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,511 copying janis_core/tests/data/galaxy/abricate/test-data/MRSA0252.fna -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,596 copying janis_core/tests/data/galaxy/abricate/test-data/output_db-card.txt -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,602 copying janis_core/tests/data/galaxy/abricate/test-data/output_db-megares.txt -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,605 copying janis_core/tests/data/galaxy/abricate/test-data/output_gbk.txt -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,607 copying janis_core/tests/data/galaxy/abricate/test-data/output_list.txt -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,609 copying janis_core/tests/data/galaxy/abricate/test-data/output_mincov100.txt -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,611 copying janis_core/tests/data/galaxy/abricate/test-data/output_minid100.txt -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,613 copying janis_core/tests/data/galaxy/abricate/test-data/output_mrsa.txt -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,615 copying janis_core/tests/data/galaxy/abricate/test-data/output_noheader.txt -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,617 copying janis_core/tests/data/galaxy/abricate/test-data/output_noresults.txt -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,619 copying janis_core/tests/data/galaxy/abricate/test-data/output_summary.txt -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,621 copying janis_core/tests/data/galaxy/abricate/test-data/test.gbk -> build/lib/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:48:57,623 creating build/lib/janis_core/tests/data/galaxy/fastqc-5ec9f6bceaee 2023-09-27T07:48:57,625 copying janis_core/tests/data/galaxy/fastqc-5ec9f6bceaee/.hg_archival.txt -> build/lib/janis_core/tests/data/galaxy/fastqc-5ec9f6bceaee 2023-09-27T07:48:57,627 copying janis_core/tests/data/galaxy/fastqc-5ec9f6bceaee/rgFastQC.xml -> build/lib/janis_core/tests/data/galaxy/fastqc-5ec9f6bceaee 2023-09-27T07:48:57,629 creating build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d 2023-09-27T07:48:57,630 copying janis_core/tests/data/galaxy/hisat2-6c19daec423d/.hg_archival.txt -> build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d 2023-09-27T07:48:57,633 copying janis_core/tests/data/galaxy/hisat2-6c19daec423d/hisat2.xml -> build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d 2023-09-27T07:48:57,637 copying janis_core/tests/data/galaxy/hisat2-6c19daec423d/hisat2_macros.xml -> build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d 2023-09-27T07:48:57,639 copying janis_core/tests/data/galaxy/hisat2-6c19daec423d/tool_data_table_conf.xml.sample -> build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d 2023-09-27T07:48:57,642 copying janis_core/tests/data/galaxy/hisat2-6c19daec423d/tool_data_table_conf.xml.test -> build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d 2023-09-27T07:48:57,644 creating build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d/tool-data 2023-09-27T07:48:57,644 copying janis_core/tests/data/galaxy/hisat2-6c19daec423d/tool-data/hisat2_indexes.loc.sample -> build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d/tool-data 2023-09-27T07:48:57,647 creating build/lib/janis_core/tests/data/galaxy/nanoplot-edbb6c5028f5 2023-09-27T07:48:57,647 copying janis_core/tests/data/galaxy/nanoplot-edbb6c5028f5/.hg_archival.txt -> build/lib/janis_core/tests/data/galaxy/nanoplot-edbb6c5028f5 2023-09-27T07:48:57,650 copying janis_core/tests/data/galaxy/nanoplot-edbb6c5028f5/nanoplot.xml -> build/lib/janis_core/tests/data/galaxy/nanoplot-edbb6c5028f5 2023-09-27T07:48:57,653 creating build/lib/janis_core/tests/data/galaxy/quast-675488238c96 2023-09-27T07:48:57,654 copying janis_core/tests/data/galaxy/quast-675488238c96/macros.xml -> build/lib/janis_core/tests/data/galaxy/quast-675488238c96 2023-09-27T07:48:57,656 copying janis_core/tests/data/galaxy/quast-675488238c96/quast.xml -> build/lib/janis_core/tests/data/galaxy/quast-675488238c96 2023-09-27T07:48:57,659 creating build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,660 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/.hg_archival.txt -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,662 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/ansi2html.sh -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,665 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/awk.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,667 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/cat.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,669 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/cut.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,672 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/easyjoin -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,676 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/easyjoin.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,678 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/find_and_replace -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,681 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/find_and_replace.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,684 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/grep.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,689 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/head.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,691 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/macros.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,694 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/multijoin -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,697 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/multijoin.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,699 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/readme.rst -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,702 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/recurring_lines.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,704 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/replace_text_in_column.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,707 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/replace_text_in_line.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,709 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/sed.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,711 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/sort-header -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,714 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/sort.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,716 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/sort_rows.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,718 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/sorted_uniq.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,721 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/tac.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,723 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/tail.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,725 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/unfold_column.py -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,727 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/unfold_column.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,729 copying janis_core/tests/data/galaxy/text_processing-d698c222f354/unsorted_uniq.xml -> build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:48:57,732 creating build/lib/janis_core/tests/data/janis 2023-09-27T07:48:57,733 copying janis_core/tests/data/janis/test_codetool.py -> build/lib/janis_core/tests/data/janis 2023-09-27T07:48:57,735 creating build/lib/janis_core/tests/data/janis/simple 2023-09-27T07:48:57,736 copying janis_core/tests/data/janis/simple/workflow.py -> build/lib/janis_core/tests/data/janis/simple 2023-09-27T07:48:57,738 creating build/lib/janis_core/tests/data/janis/simple/scripts 2023-09-27T07:48:57,739 copying janis_core/tests/data/janis/simple/scripts/multiqc_multiqc_config -> build/lib/janis_core/tests/data/janis/simple/scripts 2023-09-27T07:48:57,741 creating build/lib/janis_core/tests/data/janis/simple/tools 2023-09-27T07:48:57,743 copying janis_core/tests/data/janis/simple/tools/fastqc.py -> build/lib/janis_core/tests/data/janis/simple/tools 2023-09-27T07:48:57,746 copying janis_core/tests/data/janis/simple/tools/multiqc.py -> build/lib/janis_core/tests/data/janis/simple/tools 2023-09-27T07:48:57,748 copying janis_core/tests/data/janis/simple/tools/prokka.py -> build/lib/janis_core/tests/data/janis/simple/tools 2023-09-27T07:48:57,751 copying janis_core/tests/data/janis/simple/tools/quast.py -> build/lib/janis_core/tests/data/janis/simple/tools 2023-09-27T07:48:57,753 copying janis_core/tests/data/janis/simple/tools/unicycler.py -> build/lib/janis_core/tests/data/janis/simple/tools 2023-09-27T07:48:57,756 creating build/lib/janis_core/tests/data/janis/simple_truncated 2023-09-27T07:48:57,756 creating build/lib/janis_core/tests/data/janis/simple_truncated/scripts 2023-09-27T07:48:57,757 copying janis_core/tests/data/janis/simple_truncated/scripts/multiqc_multiqc_config -> build/lib/janis_core/tests/data/janis/simple_truncated/scripts 2023-09-27T07:48:57,759 creating build/lib/janis_core/tests/data/janis/simple_truncated/tools 2023-09-27T07:48:57,760 copying janis_core/tests/data/janis/simple_truncated/tools/multiqc.py -> build/lib/janis_core/tests/data/janis/simple_truncated/tools 2023-09-27T07:48:57,762 copying janis_core/tests/data/janis/simple_truncated/tools/prokka.py -> build/lib/janis_core/tests/data/janis/simple_truncated/tools 2023-09-27T07:48:57,765 copying janis_core/tests/data/janis/simple_truncated/tools/quast.py -> build/lib/janis_core/tests/data/janis/simple_truncated/tools 2023-09-27T07:48:57,767 creating build/lib/janis_core/tests/data/janis/wgs_somatic_dep 2023-09-27T07:48:57,768 copying janis_core/tests/data/janis/wgs_somatic_dep/__init__.py -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep 2023-09-27T07:48:57,770 copying janis_core/tests/data/janis/wgs_somatic_dep/wgssomatic.py -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep 2023-09-27T07:48:57,773 copying janis_core/tests/data/janis/wgs_somatic_dep/wgssomatic_variantsonly.py -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep 2023-09-27T07:48:57,775 creating build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl 2023-09-27T07:48:57,776 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/WGSSomaticMultiCallers-inp.yml -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl 2023-09-27T07:48:57,779 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/WGSSomaticMultiCallers_1_4_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl 2023-09-27T07:48:57,781 creating build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,782 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/AddBamStatsSomatic_v0_1_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,785 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/BwaAligner_1_0_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,787 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/BwaMemSamtoolsView_0_7_17_1_9.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,790 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/ConcatStrelkaSomaticVcf_0_1_16.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,792 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/FilterVardictSomaticVcf_v1_9.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,794 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/GATK4_SomaticVariantCaller_4_1_3_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,797 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/GATKBaseRecalBQSRWorkflow_4_1_3.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,799 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4ApplyBQSR_4_1_3_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,801 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4BaseRecalibrator_4_1_3_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,804 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4CalculateContamination_4_1_4_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,806 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4CollectInsertSizeMetrics_4_1_3_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,809 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4FilterMutectCalls_4_1_3_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,811 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4GatherVcfs_4_1_3_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,814 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4GetPileupSummaries_4_1_6_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,817 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4LearnReadOrientationModel_4_1_4_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,820 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4MarkDuplicates_4_1_3_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,823 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4MergeSamFiles_4_1_3_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,825 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4Mutect2_4_1_3_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,829 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4SortSam_4_1_2_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,831 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4SplitReads_4_1_3_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,835 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/GenerateGenomeFileForBedtoolsCoverage_v0_1_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,838 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/GenerateVardictHeaderLines_v0_1_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,841 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/ParseFastqcAdaptors_v0_1_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,844 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/PerformanceSummaryGenome_v0_1_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,846 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/SamToolsFlagstat_1_9_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,848 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/SamToolsMpileup_1_9_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,851 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/SamToolsView_1_9_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,854 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/SplitMultiAllele_v0_5772.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,856 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/UncompressArchive_v1_0_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,859 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/VcfTools_0_1_16.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,861 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/addBamStats_0_0_7.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,863 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/bcftoolsAnnotate_v1_5.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,866 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/bcftoolssort_v1_9.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,868 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/bedtoolsgenomeCoverageBed_v2_29_2.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,871 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/bgzip_1_2_1.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,873 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/combinevariants_0_0_8.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,875 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/cutadapt_2_1.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,878 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/extractStrelkaSomaticADDP_0_1_1.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,880 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/fastqc_v0_11_8.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,883 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/gridss_v2_6_2.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,885 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/manta_1_5_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,888 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/mergeAndMarkBams_4_1_3.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,890 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/performanceSummary_0_0_7.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,892 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/samtools_mpileup_subpipeline.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,895 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/somatic_subpipeline.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,897 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/split_bam_subpipeline.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,900 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/strelkaSomaticVariantCaller_v0_1_1.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,903 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/strelka_somatic_2_9_10.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,907 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/tabix_1_2_1.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,910 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/trimIUPAC_0_0_5.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,913 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/vardictSomaticVariantCaller_v0_1_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,915 copying janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/vardict_somatic_1_6_0.cwl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:57,919 creating build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl 2023-09-27T07:48:57,920 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/WGSSomaticMultiCallers-inp.json -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl 2023-09-27T07:48:57,924 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/WGSSomaticMultiCallers_1_4_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl 2023-09-27T07:48:57,928 creating build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,929 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/AddBamStatsSomatic_v0_1_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,933 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/BwaAligner_1_0_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,935 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/BwaMemSamtoolsView_0_7_17_1_9.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,938 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/ConcatStrelkaSomaticVcf_0_1_16.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,942 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/FilterVardictSomaticVcf_v1_9.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,945 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/GATK4_SomaticVariantCaller_4_1_3_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,949 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/GATKBaseRecalBQSRWorkflow_4_1_3.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,952 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4ApplyBQSR_4_1_3_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,956 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4BaseRecalibrator_4_1_3_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,959 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4CalculateContamination_4_1_4_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,962 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4CollectInsertSizeMetrics_4_1_3_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,966 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4FilterMutectCalls_4_1_3_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,969 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4GatherVcfs_4_1_3_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,973 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4GetPileupSummaries_4_1_6_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,976 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4LearnReadOrientationModel_4_1_4_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,980 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4MarkDuplicates_4_1_3_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,984 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4MergeSamFiles_4_1_3_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,987 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4Mutect2_4_1_3_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,992 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4SortSam_4_1_2_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,995 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4SplitReads_4_1_3_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:57,999 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/GenerateGenomeFileForBedtoolsCoverage_v0_1_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,003 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/GenerateVardictHeaderLines_v0_1_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,008 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/ParseFastqcAdaptors_v0_1_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,012 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/PerformanceSummaryGenome_v0_1_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,015 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/SamToolsFlagstat_1_9_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,018 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/SamToolsMpileup_1_9_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,022 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/SamToolsView_1_9_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,026 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/SplitMultiAllele_v0_5772.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,029 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/UncompressArchive_v1_0_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,032 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/VcfTools_0_1_16.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,035 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/addBamStats_0_0_7.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,038 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/bcftoolsAnnotate_v1_5.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,040 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/bcftoolssort_v1_9.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,043 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/bedtoolsgenomeCoverageBed_v2_29_2.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,046 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/bgzip_1_2_1.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,048 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/combinevariants_0_0_8.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,051 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/cutadapt_2_1.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,054 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/extractStrelkaSomaticADDP_0_1_1.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,057 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/fastqc_v0_11_8.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,059 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/gridss_v2_6_2.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,062 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/manta_1_5_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,065 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/mergeAndMarkBams_4_1_3.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,068 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/performanceSummary_0_0_7.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,070 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/samtools_mpileup_subpipeline.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,073 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/somatic_subpipeline.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,076 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/split_bam_subpipeline.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,078 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/strelkaSomaticVariantCaller_v0_1_1.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,081 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/strelka_somatic_2_9_10.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,084 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/tabix_1_2_1.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,087 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/trimIUPAC_0_0_5.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,089 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/vardictSomaticVariantCaller_v0_1_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,092 copying janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/vardict_somatic_1_6_0.wdl -> build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:58,095 creating build/lib/janis_core/tests/data/wdl 2023-09-27T07:48:58,096 copying janis_core/tests/data/wdl/Multisample_jointgt_GATK4.wdl -> build/lib/janis_core/tests/data/wdl 2023-09-27T07:48:58,100 copying janis_core/tests/data/wdl/bwa.wdl -> build/lib/janis_core/tests/data/wdl 2023-09-27T07:48:58,103 copying janis_core/tests/data/wdl/somatic_wf.wdl -> build/lib/janis_core/tests/data/wdl 2023-09-27T07:48:58,108 copying janis_core/ingestion/galaxy/internal_model/workflow/step/post_step.txt -> build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:58,110 copying janis_core/tests/integration/README.md -> build/lib/janis_core/tests/integration 2023-09-27T07:48:58,187 installing to build/bdist.linux-armv7l/wheel 2023-09-27T07:48:58,188 running install 2023-09-27T07:48:58,211 running install_lib 2023-09-27T07:48:58,215 creating build/bdist.linux-armv7l 2023-09-27T07:48:58,215 creating build/bdist.linux-armv7l/wheel 2023-09-27T07:48:58,217 creating build/bdist.linux-armv7l/wheel/janis_core 2023-09-27T07:48:58,219 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion 2023-09-27T07:48:58,220 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl 2023-09-27T07:48:58,221 copying build/lib/janis_core/ingestion/cwl/identifiers.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl 2023-09-27T07:48:58,223 copying build/lib/janis_core/ingestion/cwl/expressions.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl 2023-09-27T07:48:58,226 copying build/lib/janis_core/ingestion/cwl/main.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl 2023-09-27T07:48:58,229 copying build/lib/janis_core/ingestion/cwl/graph.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl 2023-09-27T07:48:58,231 copying build/lib/janis_core/ingestion/cwl/types.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl 2023-09-27T07:48:58,235 copying build/lib/janis_core/ingestion/cwl/preprocessing.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl 2023-09-27T07:48:58,239 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl/parsing 2023-09-27T07:48:58,240 copying build/lib/janis_core/ingestion/cwl/parsing/tool.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl/parsing 2023-09-27T07:48:58,244 copying build/lib/janis_core/ingestion/cwl/parsing/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl/parsing 2023-09-27T07:48:58,246 copying build/lib/janis_core/ingestion/cwl/parsing/workflow.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl/parsing 2023-09-27T07:48:58,250 copying build/lib/janis_core/ingestion/cwl/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl 2023-09-27T07:48:58,253 copying build/lib/janis_core/ingestion/cwl/loading.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/cwl 2023-09-27T07:48:58,257 copying build/lib/janis_core/ingestion/main.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion 2023-09-27T07:48:58,262 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/data 2023-09-27T07:48:58,263 copying build/lib/janis_core/ingestion/data/logging_config.yaml -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/data 2023-09-27T07:48:58,266 copying build/lib/janis_core/ingestion/data/janis_types.yaml -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/data 2023-09-27T07:48:58,275 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/data/galaxy 2023-09-27T07:48:58,278 copying build/lib/janis_core/ingestion/data/galaxy/galaxy_config.yaml -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/data/galaxy 2023-09-27T07:48:58,285 copying build/lib/janis_core/ingestion/data/galaxy/datatypes_conf.xml.sample -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/data/galaxy 2023-09-27T07:48:58,336 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/wdl 2023-09-27T07:48:58,336 copying build/lib/janis_core/ingestion/wdl/main.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/wdl 2023-09-27T07:48:58,339 copying build/lib/janis_core/ingestion/wdl/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/wdl 2023-09-27T07:48:58,340 copying build/lib/janis_core/ingestion/SupportedIngestion.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion 2023-09-27T07:48:58,343 copying build/lib/janis_core/ingestion/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion 2023-09-27T07:48:58,346 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy 2023-09-27T07:48:58,347 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow 2023-09-27T07:48:58,349 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/connections 2023-09-27T07:48:58,350 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/connections/scatter.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/connections 2023-09-27T07:48:58,352 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/connections/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/connections 2023-09-27T07:48:58,354 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/updates 2023-09-27T07:48:58,355 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/updates/optionality.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/updates 2023-09-27T07:48:58,357 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/updates/main.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/updates 2023-09-27T07:48:58,359 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/updates/arrays.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/updates 2023-09-27T07:48:58,361 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/updates/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/updates 2023-09-27T07:48:58,363 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/updates/datatypes.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/updates 2023-09-27T07:48:58,365 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/tool_state 2023-09-27T07:48:58,366 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/tool_state/filters.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/tool_state 2023-09-27T07:48:58,368 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/tool_state/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/tool_state 2023-09-27T07:48:58,370 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/tool_state/load.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/tool_state 2023-09-27T07:48:58,372 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/parsing 2023-09-27T07:48:58,373 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step 2023-09-27T07:48:58,374 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/metadata.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step 2023-09-27T07:48:58,376 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/tool.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step 2023-09-27T07:48:58,378 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step 2023-09-27T07:48:58,380 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/outputs.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step 2023-09-27T07:48:58,382 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/prepost.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step 2023-09-27T07:48:58,383 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/metadata.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/parsing 2023-09-27T07:48:58,385 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/step.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/parsing 2023-09-27T07:48:58,387 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/inputs.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/parsing 2023-09-27T07:48:58,388 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/parsing/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/parsing 2023-09-27T07:48:58,390 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:58,391 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/values/runtime.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:58,394 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/values/factory.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:58,395 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/values/default.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:58,397 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/values/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:58,399 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/values/scripts.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:58,401 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/values/connection.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:58,402 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/values/static.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow/values 2023-09-27T07:48:58,405 copying build/lib/janis_core/ingestion/galaxy/gxworkflow/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxworkflow 2023-09-27T07:48:58,407 copying build/lib/janis_core/ingestion/galaxy/aliases.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy 2023-09-27T07:48:58,409 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:58,410 copying build/lib/janis_core/ingestion/galaxy/datatypes/main.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:58,412 copying build/lib/janis_core/ingestion/galaxy/datatypes/core.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:58,414 copying build/lib/janis_core/ingestion/galaxy/datatypes/register.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:58,415 copying build/lib/janis_core/ingestion/galaxy/datatypes/galaxy.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:58,419 copying build/lib/janis_core/ingestion/galaxy/datatypes/JanisDatatype.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:58,421 copying build/lib/janis_core/ingestion/galaxy/datatypes/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:58,422 copying build/lib/janis_core/ingestion/galaxy/datatypes/conversion.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:58,424 copying build/lib/janis_core/ingestion/galaxy/datatypes/strategies.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/datatypes 2023-09-27T07:48:58,426 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers 2023-09-27T07:48:58,428 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/requests 2023-09-27T07:48:58,429 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/requests/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/requests 2023-09-27T07:48:58,430 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/requests/versions.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/requests 2023-09-27T07:48:58,433 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:58,434 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping/wrappers.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:58,436 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping/scraping.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:58,438 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping/single.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:58,439 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping/revisions.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:58,441 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping/repositories.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:58,443 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:58,445 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/scraping/utils.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/scraping 2023-09-27T07:48:58,448 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/wrappers 2023-09-27T07:48:58,449 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/wrappers/WrapperCache.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/wrappers 2023-09-27T07:48:58,451 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/wrappers/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/wrappers 2023-09-27T07:48:58,453 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/wrappers/Wrapper.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/wrappers 2023-09-27T07:48:58,455 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/downloads 2023-09-27T07:48:58,456 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/downloads/wrappers.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/downloads 2023-09-27T07:48:58,458 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/downloads/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/downloads 2023-09-27T07:48:58,460 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/downloads/cache.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers/downloads 2023-09-27T07:48:58,461 copying build/lib/janis_core/ingestion/galaxy/gxwrappers/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxwrappers 2023-09-27T07:48:58,464 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/janis_mapping 2023-09-27T07:48:58,464 copying build/lib/janis_core/ingestion/galaxy/janis_mapping/general.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/janis_mapping 2023-09-27T07:48:58,467 copying build/lib/janis_core/ingestion/galaxy/janis_mapping/tool.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/janis_mapping 2023-09-27T07:48:58,469 copying build/lib/janis_core/ingestion/galaxy/janis_mapping/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/janis_mapping 2023-09-27T07:48:58,470 copying build/lib/janis_core/ingestion/galaxy/janis_mapping/workflow.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/janis_mapping 2023-09-27T07:48:58,473 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool 2023-09-27T07:48:58,474 copying build/lib/janis_core/ingestion/galaxy/gxtool/TestRegister.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool 2023-09-27T07:48:58,476 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:58,477 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/annotation.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:58,480 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/tokens 2023-09-27T07:48:58,481 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/tokens/factory.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/tokens 2023-09-27T07:48:58,483 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/tokens/token.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/tokens 2023-09-27T07:48:58,485 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/tokens/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/tokens 2023-09-27T07:48:58,487 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/tokens/utils.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/tokens 2023-09-27T07:48:58,489 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/tokens/prioritisation.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/tokens 2023-09-27T07:48:58,491 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/main.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:58,493 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:58,494 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/epath/Annotator.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:58,497 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/epath/analysis.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:58,499 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/epath/ComponentOrderingStrategy.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:58,501 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/epath/ExecutionPathAnnotator.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:58,503 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/epath/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:58,504 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/epath/ExecutionPath.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/epath 2023-09-27T07:48:58,506 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/tokenise.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:58,508 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/epaths.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:58,509 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/Command.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:58,512 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components 2023-09-27T07:48:58,514 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/outputs 2023-09-27T07:48:58,514 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/outputs/InputOutput.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/outputs 2023-09-27T07:48:58,516 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/outputs/WildcardOutput.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/outputs 2023-09-27T07:48:58,518 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/outputs/OutputComponent.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/outputs 2023-09-27T07:48:58,520 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/outputs/RedirectOutput.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/outputs 2023-09-27T07:48:58,522 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/outputs/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/outputs 2023-09-27T07:48:58,523 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/factory.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components 2023-09-27T07:48:58,525 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/ValueRecord.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components 2023-09-27T07:48:58,527 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/CommandComponent.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components 2023-09-27T07:48:58,529 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components 2023-09-27T07:48:58,531 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/linux 2023-09-27T07:48:58,532 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/linux/Tee.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/linux 2023-09-27T07:48:58,534 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/linux/streams.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/linux 2023-09-27T07:48:58,536 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/linux/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/linux 2023-09-27T07:48:58,538 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:58,539 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs/Option.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:58,541 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs/InputComponent.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:58,543 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs/Flag.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:58,545 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:58,546 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs/utils.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:58,548 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/components/inputs/Positional.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/components/inputs 2023-09-27T07:48:58,550 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/update.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:58,552 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:58,554 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/loading.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command 2023-09-27T07:48:58,557 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:58,557 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr/CommandString.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:58,559 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr/MainStatementInferrer.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:58,562 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr/constructs.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:58,564 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr/generate.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:58,566 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr/analysis.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:58,568 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr/RealisedTokenValues.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:58,570 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr/DynamicCommandStatement.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:58,572 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:58,574 copying build/lib/janis_core/ingestion/galaxy/gxtool/command/cmdstr/utils.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/command/cmdstr 2023-09-27T07:48:58,576 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text 2023-09-27T07:48:58,577 copying build/lib/janis_core/ingestion/galaxy/gxtool/text/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text 2023-09-27T07:48:58,579 copying build/lib/janis_core/ingestion/galaxy/gxtool/text/utils.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text 2023-09-27T07:48:58,581 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text/simplification 2023-09-27T07:48:58,582 copying build/lib/janis_core/ingestion/galaxy/gxtool/text/simplification/aliases.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text/simplification 2023-09-27T07:48:58,585 copying build/lib/janis_core/ingestion/galaxy/gxtool/text/simplification/filters.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text/simplification 2023-09-27T07:48:58,587 copying build/lib/janis_core/ingestion/galaxy/gxtool/text/simplification/simplify.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text/simplification 2023-09-27T07:48:58,588 copying build/lib/janis_core/ingestion/galaxy/gxtool/text/simplification/main_statement.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text/simplification 2023-09-27T07:48:58,591 copying build/lib/janis_core/ingestion/galaxy/gxtool/text/simplification/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text/simplification 2023-09-27T07:48:58,593 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text/cheetah 2023-09-27T07:48:58,593 copying build/lib/janis_core/ingestion/galaxy/gxtool/text/cheetah/evaluation.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text/cheetah 2023-09-27T07:48:58,595 copying build/lib/janis_core/ingestion/galaxy/gxtool/text/cheetah/blocks.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text/cheetah 2023-09-27T07:48:58,598 copying build/lib/janis_core/ingestion/galaxy/gxtool/text/cheetah/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/text/cheetah 2023-09-27T07:48:58,599 copying build/lib/janis_core/ingestion/galaxy/gxtool/mock.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool 2023-09-27T07:48:58,602 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing 2023-09-27T07:48:58,604 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:58,605 copying build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests/custom_ops.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:58,607 copying build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests/custom_preprocessors.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:58,609 copying build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests/mapper.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:58,611 copying build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests/TestFactoryOld.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:58,613 copying build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:58,614 copying build/lib/janis_core/ingestion/galaxy/gxtool/parsing/tests/checks.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing/tests 2023-09-27T07:48:58,616 copying build/lib/janis_core/ingestion/galaxy/gxtool/parsing/main.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing 2023-09-27T07:48:58,619 copying build/lib/janis_core/ingestion/galaxy/gxtool/parsing/param_flattener.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing 2023-09-27T07:48:58,621 copying build/lib/janis_core/ingestion/galaxy/gxtool/parsing/inputs.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing 2023-09-27T07:48:58,623 copying build/lib/janis_core/ingestion/galaxy/gxtool/parsing/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing 2023-09-27T07:48:58,624 copying build/lib/janis_core/ingestion/galaxy/gxtool/parsing/outputs.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/parsing 2023-09-27T07:48:58,627 copying build/lib/janis_core/ingestion/galaxy/gxtool/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool 2023-09-27T07:48:58,630 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:58,631 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/citations.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:58,633 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/requirement.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:58,635 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/metadata.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:58,637 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/tool.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:58,639 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model/params 2023-09-27T07:48:58,640 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/params/input_param.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model/params 2023-09-27T07:48:58,642 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/params/param.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model/params 2023-09-27T07:48:58,644 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/params/param_register.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model/params 2023-09-27T07:48:58,646 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/params/output_param.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model/params 2023-09-27T07:48:58,647 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/params/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model/params 2023-09-27T07:48:58,649 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/configfile.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:58,650 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:58,652 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/tests.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:58,654 copying build/lib/janis_core/ingestion/galaxy/gxtool/model/script.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/gxtool/model 2023-09-27T07:48:58,656 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model 2023-09-27T07:48:58,657 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/tool 2023-09-27T07:48:58,658 copying build/lib/janis_core/ingestion/galaxy/internal_model/tool/tool.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/tool 2023-09-27T07:48:58,660 copying build/lib/janis_core/ingestion/galaxy/internal_model/tool/generate.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/tool 2023-09-27T07:48:58,663 copying build/lib/janis_core/ingestion/galaxy/internal_model/tool/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/tool 2023-09-27T07:48:58,665 copying build/lib/janis_core/ingestion/galaxy/internal_model/tool/outputs.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/tool 2023-09-27T07:48:58,667 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow 2023-09-27T07:48:58,668 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/metadata.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow 2023-09-27T07:48:58,670 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:58,671 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step/metadata.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:58,673 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step/step.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:58,675 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step/post_step.txt -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:58,677 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step/inputs.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:58,679 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:58,680 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/step/outputs.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow/step 2023-09-27T07:48:58,682 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/input.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow 2023-09-27T07:48:58,684 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow 2023-09-27T07:48:58,686 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow/registers 2023-09-27T07:48:58,687 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/registers/StepOutputRegister.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow/registers 2023-09-27T07:48:58,689 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/registers/StepInputRegister.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow/registers 2023-09-27T07:48:58,690 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/registers/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow/registers 2023-09-27T07:48:58,692 copying build/lib/janis_core/ingestion/galaxy/internal_model/workflow/workflow.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model/workflow 2023-09-27T07:48:58,694 copying build/lib/janis_core/ingestion/galaxy/internal_model/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model 2023-09-27T07:48:58,695 copying build/lib/janis_core/ingestion/galaxy/internal_model/protocols.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_model 2023-09-27T07:48:58,698 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/runtime 2023-09-27T07:48:58,699 copying build/lib/janis_core/ingestion/galaxy/runtime/general.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/runtime 2023-09-27T07:48:58,700 copying build/lib/janis_core/ingestion/galaxy/runtime/tool.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/runtime 2023-09-27T07:48:58,702 copying build/lib/janis_core/ingestion/galaxy/runtime/dates.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/runtime 2023-09-27T07:48:58,704 copying build/lib/janis_core/ingestion/galaxy/runtime/exceptions.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/runtime 2023-09-27T07:48:58,706 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/runtime/startup 2023-09-27T07:48:58,707 copying build/lib/janis_core/ingestion/galaxy/runtime/startup/tool.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/runtime/startup 2023-09-27T07:48:58,709 copying build/lib/janis_core/ingestion/galaxy/runtime/startup/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/runtime/startup 2023-09-27T07:48:58,712 copying build/lib/janis_core/ingestion/galaxy/runtime/startup/workflow.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/runtime/startup 2023-09-27T07:48:58,714 copying build/lib/janis_core/ingestion/galaxy/runtime/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/runtime 2023-09-27T07:48:58,717 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:58,718 copying build/lib/janis_core/ingestion/galaxy/containers/Container.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:58,720 copying build/lib/janis_core/ingestion/galaxy/containers/main.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:58,722 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:58,723 copying build/lib/janis_core/ingestion/galaxy/containers/fetching/presets.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:58,725 copying build/lib/janis_core/ingestion/galaxy/containers/fetching/GA4GHFetcher.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:58,727 copying build/lib/janis_core/ingestion/galaxy/containers/fetching/ContainerReqFetcher.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:58,728 copying build/lib/janis_core/ingestion/galaxy/containers/fetching/QuayIOFetcher.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:58,730 copying build/lib/janis_core/ingestion/galaxy/containers/fetching/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:58,732 copying build/lib/janis_core/ingestion/galaxy/containers/fetching/utils.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:58,733 copying build/lib/janis_core/ingestion/galaxy/containers/fetching/Fetcher.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers/fetching 2023-09-27T07:48:58,735 copying build/lib/janis_core/ingestion/galaxy/containers/mulled.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:58,738 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers/selection 2023-09-27T07:48:58,739 copying build/lib/janis_core/ingestion/galaxy/containers/selection/selection.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers/selection 2023-09-27T07:48:58,741 copying build/lib/janis_core/ingestion/galaxy/containers/selection/VersionMatcher.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers/selection 2023-09-27T07:48:58,743 copying build/lib/janis_core/ingestion/galaxy/containers/selection/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers/selection 2023-09-27T07:48:58,744 copying build/lib/janis_core/ingestion/galaxy/containers/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:58,746 copying build/lib/janis_core/ingestion/galaxy/containers/fetch.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:58,747 copying build/lib/janis_core/ingestion/galaxy/containers/cache.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/containers 2023-09-27T07:48:58,750 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/regex_to_glob 2023-09-27T07:48:58,750 copying build/lib/janis_core/ingestion/galaxy/regex_to_glob/convert.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/regex_to_glob 2023-09-27T07:48:58,752 copying build/lib/janis_core/ingestion/galaxy/regex_to_glob/patterns.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/regex_to_glob 2023-09-27T07:48:58,754 copying build/lib/janis_core/ingestion/galaxy/regex_to_glob/common.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/regex_to_glob 2023-09-27T07:48:58,756 copying build/lib/janis_core/ingestion/galaxy/regex_to_glob/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/regex_to_glob 2023-09-27T07:48:58,757 copying build/lib/janis_core/ingestion/galaxy/logging.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy 2023-09-27T07:48:58,759 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/tags 2023-09-27T07:48:58,760 copying build/lib/janis_core/ingestion/galaxy/tags/groups.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/tags 2023-09-27T07:48:58,762 copying build/lib/janis_core/ingestion/galaxy/tags/rules.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/tags 2023-09-27T07:48:58,764 copying build/lib/janis_core/ingestion/galaxy/tags/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/tags 2023-09-27T07:48:58,765 copying build/lib/janis_core/ingestion/galaxy/tags/manager.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/tags 2023-09-27T07:48:58,767 copying build/lib/janis_core/ingestion/galaxy/tags/strategies.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/tags 2023-09-27T07:48:58,768 copying build/lib/janis_core/ingestion/galaxy/ingest.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy 2023-09-27T07:48:58,771 copying build/lib/janis_core/ingestion/galaxy/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy 2023-09-27T07:48:58,773 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/utils 2023-09-27T07:48:58,774 copying build/lib/janis_core/ingestion/galaxy/utils/general.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/utils 2023-09-27T07:48:58,775 copying build/lib/janis_core/ingestion/galaxy/utils/galaxy.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/utils 2023-09-27T07:48:58,777 copying build/lib/janis_core/ingestion/galaxy/utils/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/utils 2023-09-27T07:48:58,779 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio 2023-09-27T07:48:58,780 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text 2023-09-27T07:48:58,781 copying build/lib/janis_core/ingestion/galaxy/fileio/text/TextRender.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text 2023-09-27T07:48:58,784 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:58,785 copying build/lib/janis_core/ingestion/galaxy/fileio/text/tool/ToolInputSectionText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:58,786 copying build/lib/janis_core/ingestion/galaxy/fileio/text/tool/UnstranslatedText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:58,788 copying build/lib/janis_core/ingestion/galaxy/fileio/text/tool/ToolOutputText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:58,790 copying build/lib/janis_core/ingestion/galaxy/fileio/text/tool/ToolOutputSectionText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:58,792 copying build/lib/janis_core/ingestion/galaxy/fileio/text/tool/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:58,793 copying build/lib/janis_core/ingestion/galaxy/fileio/text/tool/ToolInputText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:58,795 copying build/lib/janis_core/ingestion/galaxy/fileio/text/tool/ConfigfileText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:58,797 copying build/lib/janis_core/ingestion/galaxy/fileio/text/tool/ToolText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/tool 2023-09-27T07:48:58,798 copying build/lib/janis_core/ingestion/galaxy/fileio/text/formatting.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text 2023-09-27T07:48:58,800 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:58,801 copying build/lib/janis_core/ingestion/galaxy/fileio/text/workflow/WorkflowInputText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:58,803 copying build/lib/janis_core/ingestion/galaxy/fileio/text/workflow/StepText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:58,805 copying build/lib/janis_core/ingestion/galaxy/fileio/text/workflow/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:58,807 copying build/lib/janis_core/ingestion/galaxy/fileio/text/workflow/WorkflowText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:58,809 copying build/lib/janis_core/ingestion/galaxy/fileio/text/workflow/InputsText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:58,810 copying build/lib/janis_core/ingestion/galaxy/fileio/text/workflow/ConfigText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:58,812 copying build/lib/janis_core/ingestion/galaxy/fileio/text/workflow/WorkflowOutputText.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text/workflow 2023-09-27T07:48:58,814 copying build/lib/janis_core/ingestion/galaxy/fileio/text/ordering.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text 2023-09-27T07:48:58,816 copying build/lib/janis_core/ingestion/galaxy/fileio/text/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/text 2023-09-27T07:48:58,818 copying build/lib/janis_core/ingestion/galaxy/fileio/write.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio 2023-09-27T07:48:58,819 copying build/lib/janis_core/ingestion/galaxy/fileio/initialisation.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio 2023-09-27T07:48:58,821 copying build/lib/janis_core/ingestion/galaxy/fileio/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio 2023-09-27T07:48:58,823 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/formats 2023-09-27T07:48:58,824 copying build/lib/janis_core/ingestion/galaxy/fileio/formats/DefaultFormat.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/formats 2023-09-27T07:48:58,826 copying build/lib/janis_core/ingestion/galaxy/fileio/formats/Format.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/formats 2023-09-27T07:48:58,828 copying build/lib/janis_core/ingestion/galaxy/fileio/formats/SubworkflowFormat.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/formats 2023-09-27T07:48:58,829 copying build/lib/janis_core/ingestion/galaxy/fileio/formats/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/fileio/formats 2023-09-27T07:48:58,831 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_mapping 2023-09-27T07:48:58,832 copying build/lib/janis_core/ingestion/galaxy/internal_mapping/main.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_mapping 2023-09-27T07:48:58,834 copying build/lib/janis_core/ingestion/galaxy/internal_mapping/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/internal_mapping 2023-09-27T07:48:58,836 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/expressions 2023-09-27T07:48:58,837 copying build/lib/janis_core/ingestion/galaxy/expressions/patterns.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/expressions 2023-09-27T07:48:58,839 copying build/lib/janis_core/ingestion/galaxy/expressions/matches.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/expressions 2023-09-27T07:48:58,841 copying build/lib/janis_core/ingestion/galaxy/expressions/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/expressions 2023-09-27T07:48:58,842 copying build/lib/janis_core/ingestion/galaxy/expressions/checks.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/expressions 2023-09-27T07:48:58,844 creating build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/messages 2023-09-27T07:48:58,845 copying build/lib/janis_core/ingestion/galaxy/messages/messages.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/messages 2023-09-27T07:48:58,847 copying build/lib/janis_core/ingestion/galaxy/messages/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/messages 2023-09-27T07:48:58,848 copying build/lib/janis_core/ingestion/galaxy/messages/logs.py -> build/bdist.linux-armv7l/wheel/janis_core/ingestion/galaxy/messages 2023-09-27T07:48:58,851 creating build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:48:58,852 creating build/bdist.linux-armv7l/wheel/janis_core/tests/testtools 2023-09-27T07:48:58,853 copying build/lib/janis_core/tests/testtools/components.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testtools 2023-09-27T07:48:58,855 copying build/lib/janis_core/tests/testtools/misc_commandtools.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testtools 2023-09-27T07:48:58,857 copying build/lib/janis_core/tests/testtools/bwamem.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testtools 2023-09-27T07:48:58,860 copying build/lib/janis_core/tests/testtools/fastqc.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testtools 2023-09-27T07:48:58,862 copying build/lib/janis_core/tests/testtools/gridss.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testtools 2023-09-27T07:48:58,864 copying build/lib/janis_core/tests/testtools/misc_codetools.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testtools 2023-09-27T07:48:58,866 copying build/lib/janis_core/tests/testtools/unicycler.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testtools 2023-09-27T07:48:58,868 copying build/lib/janis_core/tests/testtools/types.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testtools 2023-09-27T07:48:58,870 copying build/lib/janis_core/tests/testtools/basics.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testtools 2023-09-27T07:48:58,872 copying build/lib/janis_core/tests/testtools/arrays.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testtools 2023-09-27T07:48:58,874 copying build/lib/janis_core/tests/testtools/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testtools 2023-09-27T07:48:58,876 copying build/lib/janis_core/tests/test_janis_translate.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:48:58,879 copying build/lib/janis_core/tests/test_tools.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:48:58,881 creating build/bdist.linux-armv7l/wheel/janis_core/tests/mock 2023-09-27T07:48:58,882 copying build/lib/janis_core/tests/mock/mock_workflow.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/mock 2023-09-27T07:48:58,884 creating build/bdist.linux-armv7l/wheel/janis_core/tests/mock/cwl 2023-09-27T07:48:58,885 copying build/lib/janis_core/tests/mock/cwl/workflows.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/mock/cwl 2023-09-27T07:48:58,887 copying build/lib/janis_core/tests/mock/cwl/tools.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/mock/cwl 2023-09-27T07:48:58,888 copying build/lib/janis_core/tests/mock/cwl/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/mock/cwl 2023-09-27T07:48:58,890 copying build/lib/janis_core/tests/mock/mock_xmltool.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/mock 2023-09-27T07:48:58,892 copying build/lib/janis_core/tests/mock/mock_params.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/mock 2023-09-27T07:48:58,894 copying build/lib/janis_core/tests/mock/mock_entities.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/mock 2023-09-27T07:48:58,895 copying build/lib/janis_core/tests/mock/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/mock 2023-09-27T07:48:58,897 copying build/lib/janis_core/tests/mock/mock_tool.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/mock 2023-09-27T07:48:58,898 copying build/lib/janis_core/tests/mock/mock_components.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/mock 2023-09-27T07:48:58,900 copying build/lib/janis_core/tests/mock/mock_metadata.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/mock 2023-09-27T07:48:58,901 copying build/lib/janis_core/tests/test_validateinputvalue.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:48:58,903 creating build/bdist.linux-armv7l/wheel/janis_core/tests/integration 2023-09-27T07:48:58,904 copying build/lib/janis_core/tests/integration/test_directorygenerator.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/integration 2023-09-27T07:48:58,906 copying build/lib/janis_core/tests/integration/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/integration 2023-09-27T07:48:58,907 copying build/lib/janis_core/tests/integration/README.md -> build/bdist.linux-armv7l/wheel/janis_core/tests/integration 2023-09-27T07:48:58,909 copying build/lib/janis_core/tests/test_logger.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:48:58,911 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data 2023-09-27T07:48:58,912 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis 2023-09-27T07:48:58,913 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple 2023-09-27T07:48:58,915 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple/scripts 2023-09-27T07:48:58,916 copying build/lib/janis_core/tests/data/janis/simple/scripts/multiqc_multiqc_config -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple/scripts 2023-09-27T07:48:58,918 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple/tools 2023-09-27T07:48:58,919 copying build/lib/janis_core/tests/data/janis/simple/tools/fastqc.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple/tools 2023-09-27T07:48:58,921 copying build/lib/janis_core/tests/data/janis/simple/tools/unicycler.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple/tools 2023-09-27T07:48:58,923 copying build/lib/janis_core/tests/data/janis/simple/tools/quast.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple/tools 2023-09-27T07:48:58,926 copying build/lib/janis_core/tests/data/janis/simple/tools/prokka.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple/tools 2023-09-27T07:48:58,928 copying build/lib/janis_core/tests/data/janis/simple/tools/multiqc.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple/tools 2023-09-27T07:48:58,930 copying build/lib/janis_core/tests/data/janis/simple/workflow.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple 2023-09-27T07:48:58,932 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple_truncated 2023-09-27T07:48:58,933 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple_truncated/scripts 2023-09-27T07:48:58,935 copying build/lib/janis_core/tests/data/janis/simple_truncated/scripts/multiqc_multiqc_config -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple_truncated/scripts 2023-09-27T07:48:58,937 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple_truncated/tools 2023-09-27T07:48:58,938 copying build/lib/janis_core/tests/data/janis/simple_truncated/tools/quast.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple_truncated/tools 2023-09-27T07:48:58,941 copying build/lib/janis_core/tests/data/janis/simple_truncated/tools/prokka.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple_truncated/tools 2023-09-27T07:48:58,943 copying build/lib/janis_core/tests/data/janis/simple_truncated/tools/multiqc.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/simple_truncated/tools 2023-09-27T07:48:58,945 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep 2023-09-27T07:48:58,946 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl 2023-09-27T07:48:58,947 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/WGSSomaticMultiCallers-inp.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl 2023-09-27T07:48:58,949 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/WGSSomaticMultiCallers_1_4_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl 2023-09-27T07:48:58,952 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,953 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4MergeSamFiles_4_1_3_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,955 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4SortSam_4_1_2_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,957 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/ParseFastqcAdaptors_v0_1_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,959 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/manta_1_5_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,961 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/fastqc_v0_11_8.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,964 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4LearnReadOrientationModel_4_1_4_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,966 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/GATK4_SomaticVariantCaller_4_1_3_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,968 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/GATKBaseRecalBQSRWorkflow_4_1_3.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,970 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/extractStrelkaSomaticADDP_0_1_1.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,971 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/cutadapt_2_1.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,974 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/tabix_1_2_1.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,976 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/gridss_v2_6_2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,978 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4GetPileupSummaries_4_1_6_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,980 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/PerformanceSummaryGenome_v0_1_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,982 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/bgzip_1_2_1.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,984 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/performanceSummary_0_0_7.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,985 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/bcftoolssort_v1_9.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,987 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4SplitReads_4_1_3_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,989 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/split_bam_subpipeline.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,991 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/VcfTools_0_1_16.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,993 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4MarkDuplicates_4_1_3_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,995 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/bedtoolsgenomeCoverageBed_v2_29_2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,997 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/AddBamStatsSomatic_v0_1_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:58,999 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/vardict_somatic_1_6_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,001 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/SamToolsView_1_9_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,003 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/FilterVardictSomaticVcf_v1_9.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,005 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/SamToolsMpileup_1_9_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,007 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/strelkaSomaticVariantCaller_v0_1_1.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,009 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/vardictSomaticVariantCaller_v0_1_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,011 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/somatic_subpipeline.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,013 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/addBamStats_0_0_7.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,014 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4GatherVcfs_4_1_3_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,017 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/strelka_somatic_2_9_10.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,019 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/combinevariants_0_0_8.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,021 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/BwaAligner_1_0_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,025 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4CollectInsertSizeMetrics_4_1_3_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,027 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4FilterMutectCalls_4_1_3_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,029 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/trimIUPAC_0_0_5.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,030 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4ApplyBQSR_4_1_3_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,032 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4Mutect2_4_1_3_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,035 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4BaseRecalibrator_4_1_3_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,037 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4CalculateContamination_4_1_4_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,039 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/bcftoolsAnnotate_v1_5.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,041 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/SplitMultiAllele_v0_5772.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,043 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/ConcatStrelkaSomaticVcf_0_1_16.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,045 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/SamToolsFlagstat_1_9_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,046 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/UncompressArchive_v1_0_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,048 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/GenerateVardictHeaderLines_v0_1_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,050 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/samtools_mpileup_subpipeline.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,052 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/BwaMemSamtoolsView_0_7_17_1_9.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,054 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/GenerateGenomeFileForBedtoolsCoverage_v0_1_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,056 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/mergeAndMarkBams_4_1_3.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools 2023-09-27T07:48:59,057 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wgssomatic.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep 2023-09-27T07:48:59,060 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wgssomatic_variantsonly.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep 2023-09-27T07:48:59,062 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl 2023-09-27T07:48:59,063 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/WGSSomaticMultiCallers-inp.json -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl 2023-09-27T07:48:59,066 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,067 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/AddBamStatsSomatic_v0_1_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,069 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/VcfTools_0_1_16.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,070 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/vardictSomaticVariantCaller_v0_1_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,072 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/bcftoolssort_v1_9.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,074 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/vardict_somatic_1_6_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,076 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/split_bam_subpipeline.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,078 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/strelkaSomaticVariantCaller_v0_1_1.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,080 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/gridss_v2_6_2.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,082 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/manta_1_5_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,084 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/GATKBaseRecalBQSRWorkflow_4_1_3.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,085 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4CalculateContamination_4_1_4_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,087 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/BwaAligner_1_0_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,089 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4SplitReads_4_1_3_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,091 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4MergeSamFiles_4_1_3_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,093 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/bcftoolsAnnotate_v1_5.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,095 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/SamToolsView_1_9_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,097 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/FilterVardictSomaticVcf_v1_9.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,098 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4MarkDuplicates_4_1_3_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,100 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/BwaMemSamtoolsView_0_7_17_1_9.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,102 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/SplitMultiAllele_v0_5772.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,104 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/ParseFastqcAdaptors_v0_1_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,106 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/bedtoolsgenomeCoverageBed_v2_29_2.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,108 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4FilterMutectCalls_4_1_3_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,110 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4BaseRecalibrator_4_1_3_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,112 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4GatherVcfs_4_1_3_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,114 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/somatic_subpipeline.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,115 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/PerformanceSummaryGenome_v0_1_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,117 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/extractStrelkaSomaticADDP_0_1_1.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,119 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/samtools_mpileup_subpipeline.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,121 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/trimIUPAC_0_0_5.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,122 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/GenerateVardictHeaderLines_v0_1_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,124 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/performanceSummary_0_0_7.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,126 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/mergeAndMarkBams_4_1_3.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,128 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/SamToolsFlagstat_1_9_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,130 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/SamToolsMpileup_1_9_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,132 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4Mutect2_4_1_3_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,134 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4LearnReadOrientationModel_4_1_4_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,136 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/UncompressArchive_v1_0_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,138 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/ConcatStrelkaSomaticVcf_0_1_16.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,140 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4ApplyBQSR_4_1_3_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,142 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4GetPileupSummaries_4_1_6_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,143 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/strelka_somatic_2_9_10.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,149 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/fastqc_v0_11_8.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,150 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/GenerateGenomeFileForBedtoolsCoverage_v0_1_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,152 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4CollectInsertSizeMetrics_4_1_3_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,154 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4SortSam_4_1_2_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,156 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/bgzip_1_2_1.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,158 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/addBamStats_0_0_7.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,160 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/GATK4_SomaticVariantCaller_4_1_3_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,162 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/combinevariants_0_0_8.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,164 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/tabix_1_2_1.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,166 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/cutadapt_2_1.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools 2023-09-27T07:48:59,168 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/wdl/WGSSomaticMultiCallers_1_4_0.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep/wdl 2023-09-27T07:48:59,170 copying build/lib/janis_core/tests/data/janis/wgs_somatic_dep/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis/wgs_somatic_dep 2023-09-27T07:48:59,172 copying build/lib/janis_core/tests/data/janis/test_codetool.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/janis 2023-09-27T07:48:59,173 copying build/lib/janis_core/tests/data/aln.sorted.bam.bai -> build/bdist.linux-armv7l/wheel/janis_core/tests/data 2023-09-27T07:48:59,175 copying build/lib/janis_core/tests/data/aln.sorted.bam -> build/bdist.linux-armv7l/wheel/janis_core/tests/data 2023-09-27T07:48:59,204 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl 2023-09-27T07:48:59,206 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools 2023-09-27T07:48:59,207 copying build/lib/janis_core/tests/data/cwl/tools/BasicTestTool.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools 2023-09-27T07:48:59,209 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/datatypes 2023-09-27T07:48:59,210 copying build/lib/janis_core/tests/data/cwl/tools/datatypes/secondary_types.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/datatypes 2023-09-27T07:48:59,212 copying build/lib/janis_core/tests/data/cwl/tools/datatypes/array_types.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/datatypes 2023-09-27T07:48:59,214 copying build/lib/janis_core/tests/data/cwl/tools/datatypes/basic_types.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/datatypes 2023-09-27T07:48:59,215 copying build/lib/janis_core/tests/data/cwl/tools/bwamem.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools 2023-09-27T07:48:59,218 copying build/lib/janis_core/tests/data/cwl/tools/gatk_haplotype_caller_long.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools 2023-09-27T07:48:59,221 copying build/lib/janis_core/tests/data/cwl/tools/echo.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools 2023-09-27T07:48:59,223 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:59,224 copying build/lib/janis_core/tests/data/cwl/tools/requirements/prepare_fasta_db.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:59,226 copying build/lib/janis_core/tests/data/cwl/tools/requirements/return_directory.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:59,228 copying build/lib/janis_core/tests/data/cwl/tools/requirements/antismash_v4.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:59,229 copying build/lib/janis_core/tests/data/cwl/tools/requirements/control-freec-11-6-sbg.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:59,233 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/requirements/Python 2023-09-27T07:48:59,234 copying build/lib/janis_core/tests/data/cwl/tools/requirements/Python/add_crossmapped2resmapped.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/requirements/Python 2023-09-27T07:48:59,236 copying build/lib/janis_core/tests/data/cwl/tools/requirements/Python/check_threshold.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/requirements/Python 2023-09-27T07:48:59,239 copying build/lib/janis_core/tests/data/cwl/tools/requirements/amplicon_architect.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:59,242 copying build/lib/janis_core/tests/data/cwl/tools/requirements/bundle_secondaryfiles.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:59,244 copying build/lib/janis_core/tests/data/cwl/tools/requirements/add_crossmapped2resmapped.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:59,246 copying build/lib/janis_core/tests/data/cwl/tools/requirements/check_threshold.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/requirements 2023-09-27T07:48:59,247 copying build/lib/janis_core/tests/data/cwl/tools/rename_png.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools 2023-09-27T07:48:59,249 copying build/lib/janis_core/tests/data/cwl/tools/rose.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools 2023-09-27T07:48:59,251 copying build/lib/janis_core/tests/data/cwl/tools/fastqc.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools 2023-09-27T07:48:59,252 copying build/lib/janis_core/tests/data/cwl/tools/samtools_flagstat.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools 2023-09-27T07:48:59,254 copying build/lib/janis_core/tests/data/cwl/tools/fastqc2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools 2023-09-27T07:48:59,257 copying build/lib/janis_core/tests/data/cwl/tools/gatk_haplotype_caller.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools 2023-09-27T07:48:59,259 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/expressions 2023-09-27T07:48:59,260 copying build/lib/janis_core/tests/data/cwl/tools/expressions/streams.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/expressions 2023-09-27T07:48:59,262 copying build/lib/janis_core/tests/data/cwl/tools/expressions/inputs_arguments.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/expressions 2023-09-27T07:48:59,263 copying build/lib/janis_core/tests/data/cwl/tools/expressions/outputs.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/expressions 2023-09-27T07:48:59,265 copying build/lib/janis_core/tests/data/cwl/tools/expressions/resources.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/expressions 2023-09-27T07:48:59,267 copying build/lib/janis_core/tests/data/cwl/tools/expressions/requirements.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/expressions 2023-09-27T07:48:59,269 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/expressiontools 2023-09-27T07:48:59,270 copying build/lib/janis_core/tests/data/cwl/tools/expressiontools/check_value.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/tools/expressiontools 2023-09-27T07:48:59,273 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows 2023-09-27T07:48:59,274 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants 2023-09-27T07:48:59,276 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,277 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/gridss.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,279 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/collapse.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,280 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_view_sam2bam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,282 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_sort.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,284 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/gridss_filter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,286 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/structural_variants.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,288 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_mem_paired.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,290 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/exome_depth_filter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,291 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,293 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/manta.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,295 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/bgzip.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,297 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_merge.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,299 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/manta_filter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,300 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/gunzip.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,302 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/tabix.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,304 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/bedops_union.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,306 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_view.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,308 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/fastqc.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,310 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_mem_paired_grace.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,311 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/codex.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,314 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_mem_unpaired.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,315 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_faidx.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,317 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/codex_filter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,319 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_mem_unpaired_grace.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,321 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/tools_list.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,323 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,325 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/exome_depth.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,327 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_index_grace.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,329 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/bundle_secondaryfiles.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,330 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/unicycler.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,333 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/batch_parser.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,334 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/picard_markduplicates.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,336 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/svtools.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,338 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/merge_all.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,340 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/tools/fastp.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/tools 2023-09-27T07:48:59,342 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/workflow.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants 2023-09-27T07:48:59,343 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/workflow.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants 2023-09-27T07:48:59,346 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,347 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/samtools_view_sam2bam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,349 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/samtools_sort.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,351 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/final_filtering.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,353 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/indexing_bed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,355 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/indexing_bed.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,357 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/bam_filtering.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,358 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/cnv_exome_depth.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,360 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/bwa_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,362 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/cnv_gridss.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,364 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/cnv_codex.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,366 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/cnv_manta.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,368 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/bwa_mem.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,370 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/picard_markduplicates.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,372 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/trimmed_fastq.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows 2023-09-27T07:48:59,375 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,376 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/gridss.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,378 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/collapse.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,380 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_view_sam2bam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,381 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_sort.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,383 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/gridss_filter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,385 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/structural_variants.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,387 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bwa_mem_paired.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,389 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/exome_depth_filter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,391 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,393 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/manta.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,394 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bgzip.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,396 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_merge.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,398 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/manta_filter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,400 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/gunzip.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,401 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/tabix.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,404 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bedops_union.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,405 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_view.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,407 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/fastqc.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,410 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,410 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/samtools_view_sam2bam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,413 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/samtools_sort.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,414 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/final_filtering.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,416 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/indexing_bed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,418 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/bam_filtering.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,420 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/cnv_exome_depth.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,422 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/bwa_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,424 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/cnv_gridss.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,426 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/cnv_codex.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,428 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/cnv_manta.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,429 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/bwa_mem.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,431 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/picard_markduplicates.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,433 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/trimmed_fastq.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows 2023-09-27T07:48:59,435 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/codex.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,437 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bwa_mem_unpaired.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,439 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_faidx.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,441 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/codex_filter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,444 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bwa_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,446 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/exome_depth.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,448 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bundle_secondaryfiles.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,450 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/batch_parser.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,452 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/picard_markduplicates.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,454 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/svtools.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,456 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/merge_all.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,458 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/fastp.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations 2023-09-27T07:48:59,460 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_workflow 2023-09-27T07:48:59,460 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_workflow/abstract_workflow.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants/abstract_workflow 2023-09-27T07:48:59,463 copying build/lib/janis_core/tests/data/cwl/workflows/structuralvariants/workflow_idxs.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/structuralvariants 2023-09-27T07:48:59,465 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow 2023-09-27T07:48:59,467 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,468 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_cnvkit_batch_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,470 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_mutect2_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,472 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/control-freec-germline.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,474 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_vardict_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,476 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_production_WES_somatic_variant_cnv_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,478 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_combined_somatic_wgs_cnv_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,481 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_lancet_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,483 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_controlfreec_cnv.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,485 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_somatic_WES_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,487 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_production_WGS_somatic_variant_cnv.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,490 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/cnvkit_single_sample_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,492 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_cnv_caller_wes_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,494 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_somatic_caller_workflow.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,497 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_cnvkit_plus_theta2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated 2023-09-27T07:48:59,499 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:59,500 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/hotspot.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:59,503 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/add_strelka2_fields.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:59,505 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/sbg_multicnv.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:59,508 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/sbg_cveto_util.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:59,511 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/kf_mskcc_vcf2maf_1.6.21.pl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:59,514 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/consensus_merge.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:59,517 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/sbg_multicnv_methods.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:59,519 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/sbg_multicnv_visualisations.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts 2023-09-27T07:48:59,524 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,525 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_indexfeaturefile.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,527 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_batch.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,529 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/prep_mnp_variants.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,532 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_Mutect2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,534 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvnator.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,536 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/python_vardict_interval_split.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,538 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/snpEff_annotate.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,539 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_modelsegments.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,542 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_annotateintervals.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,544 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_filtermutectcalls.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,546 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/kf_mskcc_vcf2maf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,548 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/speedseq_sv_annotate.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,550 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_selectvariants.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,552 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/lumpy-sv_somatic.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,555 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/mode_selector.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,557 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/mode_defaults.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,560 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/expression_flatten_file_list.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,563 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/aa_classifier.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,566 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_variant_filter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,568 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/expression_flatten_list.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,570 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/awk_min_seg_length.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,573 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_collectalleliccounts.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,575 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/lancet.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,578 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/untar_gzip.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,580 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/generic_rename_outputs.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,583 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_getpileupsummaries.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,585 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/expression_run_aa_if_wgs.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,587 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_import_theta2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,589 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/add_basename.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,591 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/hotspots_annotation.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,594 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcftools_annotate.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,597 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/sb_multicnv_prepare_files_for_scatter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,599 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_plotmodeledsegments.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,602 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/tabix_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,605 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/expression_pickvalue_workaround.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,608 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/prepare_aa.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,610 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/normalize_vcf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,612 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/manta.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,615 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/sb_multicnv_1_0_0.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,618 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/add_strelka2_fields.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,620 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_plotdenoisedcopyratios.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,623 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_denoisereadcounts.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,625 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_preprocessintervals.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,628 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_calculatecontamination.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,630 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_mergevcfs.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,632 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_collectreadcounts.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,635 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_batch_only.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,637 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/ubuntu_rename_outputs.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,640 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cns_to_aa_bed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,643 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcftools_strip_ann.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,646 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/canvas_paired_wes.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,649 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/samtools_cram2bam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,651 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/sb_multicnv_rename_files.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,654 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_callcopyratiosegments.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,656 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/tar.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,658 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcbio_variant_recall_ensemble.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,660 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/theta2_purity.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,662 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/picard_createsequencedictionary.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,664 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/control-freec-11-6-sbg.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,667 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_mergemutectstats.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,668 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/samtools_faidx.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,670 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/lumpy-sv_germline.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,672 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_sortvcf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,674 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_call.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,676 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/consensus_merge.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,679 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_funcotatesegments.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,681 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/amplicon_architect.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,684 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_intervallisttool.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,686 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bwa_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,689 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_createreadcountpanelofnormals.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,691 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/strelka2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,693 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bundle_secondaryfiles.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,695 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/smoove_lumpy.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,697 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_export_theta2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,699 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_gatherpileupsummaries.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,700 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/mode_list_selector.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,702 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/variant_effect_predictor_105.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,705 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/ubuntu_ratio2seg.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,707 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_learnorientationbias.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,708 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/annotsv.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,711 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/preprocess_lancet_intervals.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,712 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/vardictjava.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,714 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcftools_reheader_vcf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,716 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/seurat.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,718 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/samtools_calmd.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,720 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/control_freec_mini_pileup.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,722 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcbio_filter_vardict_somatic.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,724 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/samtools_reheader_bam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,726 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_filter_germline_variant.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,728 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcftools_filter_vcf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,730 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bedtools_intersect.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,732 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcbio_normalize_vcf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools 2023-09-27T07:48:59,734 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated 2023-09-27T07:48:59,735 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/kfdrc_production_somatic_variant_cnv_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated 2023-09-27T07:48:59,739 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7 2023-09-27T07:48:59,740 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7/control_freec_visualize.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7 2023-09-27T07:48:59,742 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7/control_freec.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7 2023-09-27T07:48:59,744 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7/control_freec_R.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7 2023-09-27T07:48:59,746 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/samtools_cram2bam_plus_calmd.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated 2023-09-27T07:48:59,748 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config 2023-09-27T07:48:59,749 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config/control_freec_visualize.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config 2023-09-27T07:48:59,751 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config/control_freec.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config 2023-09-27T07:48:59,752 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config/control_freec_R.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config 2023-09-27T07:48:59,754 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config/gen_controlfreec_configfile.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config 2023-09-27T07:48:59,757 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,758 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/custom_split.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,760 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/quick_split_bed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,762 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/cnv_using_subwf_test.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,764 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/lancet.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,766 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/samtools_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,768 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/delme_tcga_temp_vcftomaf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,770 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/temp_rerun_vcf2maf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,772 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/gatk_sortvcf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,774 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/delme_pbta_temp_vcftomaf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,776 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/build_strelka2_mnp.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,778 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/gatk_intervallisttool.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,780 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/gen_germline_controlfreec_config.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,782 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/vardictjava.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,784 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/output_vcf_pick.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev 2023-09-27T07:48:59,786 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:59,787 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_cnvkit_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:59,789 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_controlfreec_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:59,791 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_strelka2_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:59,794 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_annot_vcf_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:59,797 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_theta2_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:59,799 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_amplicon_architect.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:48:59,802 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated 2023-09-27T07:48:59,804 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,805 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/post_processing_uniref90.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,807 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/after_qc.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,810 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cmsearch_raw_data.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,812 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/unmapped_from_pfam.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,814 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/folder_functional_annotation.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,816 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/filtering.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,817 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/pfam_domain_instances.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,819 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/change_formats_and_names.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,821 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_for_Pfam2CATH.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,823 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/functional_annotation_and_post_processing.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,825 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/pathways.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,827 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_for_CATH2Pfam.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,829 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_hmmer.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,831 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cmsearch_assembly.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,833 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_IPS.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,835 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/motus_taxonomy.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,837 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/resmapping_pfam_structs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,840 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_antismash.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,842 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/other_ncrnas.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,844 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_unite.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,846 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/diamond.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,848 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cath_domain_instances.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,850 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/classify_SSUs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,852 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/eggnog.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,854 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/unmapped_from_cath.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,856 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/overlap_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,858 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/rna_prediction.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,861 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chunking_final.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,863 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/avg_unp_domains.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,864 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_itsonedb.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,866 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_from_list.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,868 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/combined_gene_caller.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,870 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/functional_annotation.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,872 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/trimming.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,874 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/classify_LSUs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,876 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_for_core.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,878 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cgc.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,880 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/resmapping_cath_structs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,883 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/write_summaries.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,885 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/no_antismash_subwf.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,886 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/before_qc.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,889 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chunking.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,891 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/ITS.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,893 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/antismash.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,895 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/find_ribosomal_ncRNAs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows 2023-09-27T07:48:59,900 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,901 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/align_avg_structs_pairwise.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,903 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/create_csv_kp.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,905 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/split_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,907 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/counts_to_hdf5.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,909 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/per_unp_dom_instance.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,910 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_lsu_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,912 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_subunits.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,914 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/sam_to_sorted_bam.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,916 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hashsum.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,918 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/FGS.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,919 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gff.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,921 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_tax_dir.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,923 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/check_alignment_scores.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,925 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/carveme_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,927 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/length_filter.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,929 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/antismash_gff.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,930 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/smetana.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,933 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/check_threshold_step.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,935 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fastqc.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,937 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/get_ncrnas.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,938 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hashsum_paired.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,940 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_its_dir.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,942 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/clean_headers.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,944 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/copy_avg_dom.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,946 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fasta_index.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,948 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/mapseq.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,950 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/memote_run.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,952 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_chopped_structs_unp_domains.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,954 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/reformat_coords.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,956 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,957 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fix_geneclusters_txt.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,959 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/carveme.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,961 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/join.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,963 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/tohdt.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,965 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/vcf_compress.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,967 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/ngtax.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,969 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/tab_modification.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,971 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/mask_for_ITS.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,973 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_processed_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,974 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compression.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,976 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/rename_ncrnas.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,978 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_sequences.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,980 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_SSU.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,982 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unzip_merged_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,984 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/sorting.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,986 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/visualize_otu_counts.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,988 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_cds.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,989 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_seq_dir.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,991 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_reads_after_filtering.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,993 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/memote_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,995 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress_carveme.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,997 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/go_summary.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:48:59,999 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unzip_single_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,000 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/cat_models.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,002 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_files.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,004 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/header_addition.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,006 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_pfam_structures.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,008 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/per_dom_instance.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,010 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/expressiontool_bam_index.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,011 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress_mapseq.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,013 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_averaged_structures.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,015 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_LSU.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,017 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/make_tab_sep.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,019 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/QC_FLAG.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,021 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compare_instances_CATH_Pfam.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,023 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/conversion.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,025 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chop_structs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,026 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_coords.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,028 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hashsum_single.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,030 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/pairwise_align_avg_structs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,032 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/format_core_list.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,034 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/antismash_summary.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,035 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzipped_embl.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,037 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_no_antismash_flag.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,039 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/suppress_tax.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,041 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/post_processing.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,043 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/parsing_hmmscan.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,045 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/check_value.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,047 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/diamond_run.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,049 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_to_pathways_systems_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,051 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/combine.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,052 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_to_seq_cat_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,054 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gemstats.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,056 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fix_embl_and_gbk.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,058 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/calc_chunking_number.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,059 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_no_cds_flag.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,061 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/remove_overlaps.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,063 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/clean_fasta_headers.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,065 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/motus_classification.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,067 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/trim_quality_control.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,069 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_output_dir.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,071 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_ITS_seqs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,074 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_to_functional_annotation_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,076 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/genome_properties.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,078 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,080 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_antismash.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,082 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/picrust2.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,084 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chunking_tsv.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,086 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_chopped_structures_unp_domains.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,087 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/resmapping_for_Pfam_UP2PDB.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,089 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/eggnog_homology_searches.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,091 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/interproscan.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,093 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,095 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_quality_control_filtering.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,097 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/cmsearch.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,099 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gather_domain_like.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,101 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/memote_report_snapshot.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,103 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_seed_orthologs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,105 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_concatenate_matches.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,107 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gather_failed_domains.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,109 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_empty_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,111 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chinking_fasta_nucleotide.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,112 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_antismash_summary_to_pathways_systems_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,114 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/collect_lost_instances.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,116 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/folder_compression.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,118 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/functional_stats.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,120 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_lines_mapseq.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,122 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/crossmapping_CATH2Pfam.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,123 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/overlap_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,126 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/prodigal.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,127 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/add_crossmapped_to_resmapped.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,129 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/convert_trimmed_reads_to_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,131 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/kofamscan.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,133 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/reads_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,135 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_cath_structures.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,137 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/kegg_pathways.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,139 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compression_func_ann.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,141 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/pfam.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,143 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fastqc_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,144 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_concatenate_deoverlapped_matches.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,146 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/get_family_ids.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,148 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/no_tax_file_flag.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,150 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chinking_fasta_proteins.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,152 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzipped_gbk.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,154 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/ngtax_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,155 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/ngtax_to_tsv_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,157 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_submitted_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,159 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unzip.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,161 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/clean_classification.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,163 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/rename_geneclusters.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,164 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/prodigal_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,166 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/classifications_to_otu_counts.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,168 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/combine_ips.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,170 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_ssu_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,172 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_overlapped_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,174 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/qc_stats.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,176 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/add_domain_positions.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,177 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/eggnog_annotation.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,179 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/combine_trimmed.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,181 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_masked_ITS.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,183 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/resmapping_for_CATH_PDB2UP.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,186 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_geneclusters_txt.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,188 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_gbk.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,191 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/create_new_parameters.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,193 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_contigs_antismash.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,195 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_antismash_in_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,197 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chinking_SC_fasta_nucleotide.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,198 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/cat.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,201 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/crossmapping_Pfam2CATH.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,203 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/write_summaries.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,205 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_masked_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,206 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_submitted_reads_single.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,208 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/phyloseq_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,210 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chunking_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,212 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/create_csv_gp.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,214 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/picrust_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,216 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hmmsearch.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,217 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/counts_to_json.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,219 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/rename_contigs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,221 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_averaged_unp_domains.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,224 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_file_flag.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,226 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/index_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,228 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/get_coords.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,229 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress_prodigal.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,231 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/readmapping_pilon.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,233 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/pilon.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,235 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/bam_index.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,237 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_subunits_coords.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,239 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/split_seqs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,241 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_embl.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,243 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_paired.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules 2023-09-27T07:49:00,463 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/config -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated 2023-09-27T07:49:00,465 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/main.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated 2023-09-27T07:49:00,468 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_gatk_create_cnv_pon_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:49:00,470 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_lancet_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:49:00,473 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_manta_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:49:00,475 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_vardict_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:49:00,477 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/sb_multicnv_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:49:00,480 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_mutect2_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:49:00,483 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc-somatic-variant-workflow.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:49:00,486 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_consensus_calling.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:49:00,488 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_cnvkit_theta2_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow 2023-09-27T07:49:00,491 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:49:00,492 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_cnvkit_sub_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:49:00,494 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_strelka2_sub_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:49:00,497 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_gatk_cnv_somatic_pair_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:49:00,500 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_controlfreec_sub_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:49:00,502 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_manta_sub_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:49:00,504 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_mutect2_filter_support_subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:49:00,506 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_mutect2_sub_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:49:00,509 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/prepare_reference.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:49:00,511 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_run_theta2_sub_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:49:00,513 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_lancet_sub_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:49:00,515 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_vardict_sub_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows 2023-09-27T07:49:00,518 copying build/lib/janis_core/tests/data/cwl/workflows/kf-somatic-workflow/README.md -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/kf-somatic-workflow 2023-09-27T07:49:00,521 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/subworkflow_test 2023-09-27T07:49:00,522 copying build/lib/janis_core/tests/data/cwl/workflows/subworkflow_test/mandatory_input_types.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/subworkflow_test 2023-09-27T07:49:00,524 copying build/lib/janis_core/tests/data/cwl/workflows/subworkflow_test/subworkflow.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/subworkflow_test 2023-09-27T07:49:00,526 copying build/lib/janis_core/tests/data/cwl/workflows/subworkflow_test/main.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/subworkflow_test 2023-09-27T07:49:00,528 copying build/lib/janis_core/tests/data/cwl/workflows/subworkflow_test/basic.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/subworkflow_test 2023-09-27T07:49:00,529 copying build/lib/janis_core/tests/data/cwl/workflows/subworkflow_test/optional_input_types.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/subworkflow_test 2023-09-27T07:49:00,532 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics 2023-09-27T07:49:00,533 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools 2023-09-27T07:49:00,535 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats 2023-09-27T07:49:00,536 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output 2023-09-27T07:49:00,538 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:49:00,539 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/GC-distribution.out.full_bin -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:49:00,541 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/seq-length.out.full_bin -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:49:00,543 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/nucleotide-distribution.out.full -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:49:00,545 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/seq-length.out.full_pcbin -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:49:00,547 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/seq-length.out.full -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:49:00,549 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/GC-distribution.out.full_pcbin -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:49:00,550 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics/GC-distribution.out.full -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/expected-output/qc-statistics 2023-09-27T07:49:00,552 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/qc-stats.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats 2023-09-27T07:49:00,555 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/test-inputs 2023-09-27T07:49:00,556 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/test-inputs/test.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/test-inputs 2023-09-27T07:49:00,558 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/qc-stats-job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats 2023-09-27T07:49:00,560 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/MGRAST_base.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats 2023-09-27T07:49:00,562 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-stats 2023-09-27T07:49:00,565 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering 2023-09-27T07:49:00,566 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/qc-filtering-job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering 2023-09-27T07:49:00,568 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/expected-output 2023-09-27T07:49:00,569 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/expected-output/stats_summary -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/expected-output 2023-09-27T07:49:00,571 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/expected-output/test_seqs.filtered.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/expected-output 2023-09-27T07:49:00,573 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/qc-filtering.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering 2023-09-27T07:49:00,575 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/run_quality_filtering.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering 2023-09-27T07:49:00,578 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/test-input 2023-09-27T07:49:00,579 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/test-input/test_seqs.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/qc-filtering/test-input 2023-09-27T07:49:00,582 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse 2023-09-27T07:49:00,583 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/pfam_annotations.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse 2023-09-27T07:49:00,585 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/pfam_annotations.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse 2023-09-27T07:49:00,587 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/test-input 2023-09-27T07:49:00,588 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/test-input/testfile.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/test-input 2023-09-27T07:49:00,591 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/expected_output 2023-09-27T07:49:00,592 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/expected_output/testfile.annotations.pfam -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/expected_output 2023-09-27T07:49:00,595 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:49:00,596 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/format-bedfile.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:49:00,598 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/expected-output 2023-09-27T07:49:00,599 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/expected-output/ITS-maskfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/expected-output 2023-09-27T07:49:00,601 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/expected-output/masked-for-its.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/expected-output 2023-09-27T07:49:00,603 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/suppress_tax_test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:49:00,605 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/format-bedfile.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:49:00,607 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/its-length-new.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:49:00,610 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/bash_scripts 2023-09-27T07:49:00,611 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/bash_scripts/format_bedfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/bash_scripts 2023-09-27T07:49:00,613 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/suppress_tax.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:49:00,615 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input 2023-09-27T07:49:00,617 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/LSU 2023-09-27T07:49:00,618 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/LSU/LSU.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/LSU 2023-09-27T07:49:00,620 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/SSU-and-LSU -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input 2023-09-27T07:49:00,622 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/test-cmsearch.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input 2023-09-27T07:49:00,625 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/SSU 2023-09-27T07:49:00,626 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/SSU/SSU.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/test-input/SSU 2023-09-27T07:49:00,629 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/bedtools.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:49:00,631 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS/bedtools.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/mask-for-ITS 2023-09-27T07:49:00,634 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:49:00,635 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools 2023-09-27T07:49:00,636 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools/owltools -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools 2023-09-27T07:49:00,639 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools/owltools-runner-all.jar -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools 2023-09-27T07:49:01,340 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools/owltools.vmoptions -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools 2023-09-27T07:49:01,342 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go_summary.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:49:01,344 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/expected-output 2023-09-27T07:49:01,345 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/expected-output/test -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/expected-output 2023-09-27T07:49:01,347 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/expected-output/test_slim -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/expected-output 2023-09-27T07:49:01,349 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go_summary.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:49:01,351 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go-basic-metagenomics_release_20160705.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:49:01,796 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go_summary-config.json -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:49:01,798 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go-basic-metagenomics_release_20160705.obo -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:49:02,260 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go_summary_pipeline-1.0.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:49:02,263 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/metagenomics_go_slim_ids.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:49:02,265 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/test-input 2023-09-27T07:49:02,266 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/test-input/ips_out.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/test-input 2023-09-27T07:49:02,269 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/metagenomics_go_slim_banding.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:49:02,271 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim 2023-09-27T07:49:02,274 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads 2023-09-27T07:49:02,275 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs 2023-09-27T07:49:02,276 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/clean_motus_output.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs 2023-09-27T07:49:02,279 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/expected-output 2023-09-27T07:49:02,280 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/expected-output/classifications.motus.biom -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/expected-output 2023-09-27T07:49:02,317 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/mOTUs.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs 2023-09-27T07:49:02,319 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/clean_motus_output.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs 2023-09-27T07:49:02,322 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/motus-test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs 2023-09-27T07:49:02,324 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/test-input 2023-09-27T07:49:02,325 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/test-input/unpaired.fq -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Raw_reads/mOTUs/test-input 2023-09-27T07:49:02,694 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks 2023-09-27T07:49:02,699 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/split_to_chunks.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks 2023-09-27T07:49:02,719 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker 2023-09-27T07:49:02,724 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker/esl-ssplit.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker 2023-09-27T07:49:02,737 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker/fasta_chunker.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker 2023-09-27T07:49:02,744 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker/fasta_chunker.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker 2023-09-27T07:49:02,746 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker/esl-ssplit.pl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker 2023-09-27T07:49:02,749 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/dna_chunker 2023-09-27T07:49:02,751 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/expected-output-fasta_chunker 2023-09-27T07:49:02,752 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/expected-output-fasta_chunker/100_150.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/expected-output-fasta_chunker 2023-09-27T07:49:02,755 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/expected-output-fasta_chunker/1_100.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/expected-output-fasta_chunker 2023-09-27T07:49:02,758 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/protein_chunker.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks 2023-09-27T07:49:02,760 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/remove_headers.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks 2023-09-27T07:49:02,762 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/protein_chunker.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks 2023-09-27T07:49:02,764 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/remove_headers.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks 2023-09-27T07:49:02,766 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/test-input 2023-09-27T07:49:02,767 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/test-input/empty.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/chunks/test-input 2023-09-27T07:49:02,769 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan 2023-09-27T07:49:02,770 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-v5.test.job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan 2023-09-27T07:49:02,772 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-apps.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan 2023-09-27T07:49:02,774 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-v5-none_docker.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan 2023-09-27T07:49:02,775 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-protein_formats.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan 2023-09-27T07:49:02,777 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-v5.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan 2023-09-27T07:49:02,780 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:49:02,781 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries/functional_stats.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:49:02,783 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries/write_summaries.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:49:02,785 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries/write_summaries.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:49:02,786 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries/functional_stats.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:49:02,788 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries/write_summaries.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:49:02,790 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries/functional_stats.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/summaries 2023-09-27T07:49:02,792 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction 2023-09-27T07:49:02,794 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona 2023-09-27T07:49:02,795 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/expected-output 2023-09-27T07:49:02,796 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/expected-output/test.html -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/expected-output 2023-09-27T07:49:02,802 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/test-input 2023-09-27T07:49:02,803 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/test-input/test.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/test-input 2023-09-27T07:49:02,806 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/krona.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona 2023-09-27T07:49:02,808 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/krona-test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona 2023-09-27T07:49:02,810 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/krona 2023-09-27T07:49:02,813 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq 2023-09-27T07:49:02,814 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq/mapseq-test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq 2023-09-27T07:49:02,816 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq/mapseq.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq 2023-09-27T07:49:02,817 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq 2023-09-27T07:49:02,819 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap 2023-09-27T07:49:02,820 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap-v0.02.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap 2023-09-27T07:49:02,822 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap 2023-09-27T07:49:02,825 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap-v0.02.test.job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap 2023-09-27T07:49:02,827 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/test-input 2023-09-27T07:49:02,828 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/test-input/ribo.claninfo -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/test-input 2023-09-27T07:49:02,830 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/test-input/1.cmsearch.tblout -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/test-input 2023-09-27T07:49:02,835 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/expected_output 2023-09-27T07:49:02,836 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/expected_output/1.cmsearch.tblout.deoverlapped -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch-deoverlap/expected_output 2023-09-27T07:49:02,840 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords 2023-09-27T07:49:02,841 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/get_subunits_coords.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords 2023-09-27T07:49:02,843 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output 2023-09-27T07:49:02,844 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output/SSUs -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output 2023-09-27T07:49:02,846 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output/5s -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output 2023-09-27T07:49:02,848 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output/LSUs -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/expected-output 2023-09-27T07:49:02,850 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/get_subunits_coords.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords 2023-09-27T07:49:02,852 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/test-input 2023-09-27T07:49:02,853 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/test-input/matched_seqs_with_coords -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/test-input 2023-09-27T07:49:02,855 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords/get_subunits_coords.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_coords 2023-09-27T07:49:02,858 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords 2023-09-27T07:49:02,860 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/expected-output 2023-09-27T07:49:02,862 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/expected-output/matched_seqs_with_coords -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/expected-output 2023-09-27T07:49:02,864 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/awk_tool -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords 2023-09-27T07:49:02,866 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/extract-coords_awk.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords 2023-09-27T07:49:02,868 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/extract-coords_awk.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords 2023-09-27T07:49:02,870 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/test-input 2023-09-27T07:49:02,871 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/test-input/test-cmsearch.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/extract-coords/test-input 2023-09-27T07:49:02,873 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel 2023-09-27T07:49:02,875 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output 2023-09-27T07:49:02,876 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output/test.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output 2023-09-27T07:49:02,878 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output/test-cmsearch_matched_seqs_with_coords.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output 2023-09-27T07:49:02,880 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output/test.fasta.ssi -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/expected-output 2023-09-27T07:49:02,882 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-index.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel 2023-09-27T07:49:02,884 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-sfetch-index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel 2023-09-27T07:49:02,885 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-sfetch-manyseqs.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel 2023-09-27T07:49:02,887 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-sfetch-manyseqs-test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel 2023-09-27T07:49:02,889 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-sfetch-index-test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel 2023-09-27T07:49:02,891 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input 2023-09-27T07:49:02,892 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input/test.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input 2023-09-27T07:49:02,894 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input/test-cmsearch.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input 2023-09-27T07:49:02,896 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input/matched_seqs_with_coords -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/test-input 2023-09-27T07:49:02,898 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas 2023-09-27T07:49:02,900 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas/expected-output 2023-09-27T07:49:02,901 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas/expected-output/cyano_tmRNA -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas/expected-output 2023-09-27T07:49:02,903 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas/pull_ncrnas.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas 2023-09-27T07:49:02,904 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas/pull_ncrnas.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas 2023-09-27T07:49:02,906 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas/pull_ncrnas.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/pull_ncrnas 2023-09-27T07:49:02,908 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:49:02,909 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/empty_tax.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:49:02,911 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/biom-convert-table.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:49:02,913 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/empty_tax.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:49:02,915 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:49:02,916 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input/LSU_json.biom -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:49:02,918 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input/LSU.html -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:49:02,923 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input/test-mapseq.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:49:02,925 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input/LSU.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:49:02,927 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input/LSU.mseq.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:49:02,929 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input/LSU.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/input 2023-09-27T07:49:02,930 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/biom-convert_test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:49:02,932 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/empty_tax.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:49:02,934 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/biom-convert-test.job-input.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:49:02,936 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/biom-convert.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:49:02,937 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/biom-convert.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:49:02,940 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output 2023-09-27T07:49:02,941 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax 2023-09-27T07:49:02,942 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax/empty.html -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax 2023-09-27T07:49:02,948 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax/empty.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax 2023-09-27T07:49:02,949 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax/empty_json.biom -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax 2023-09-27T07:49:02,951 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax/empty.mseq.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax 2023-09-27T07:49:02,953 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert 2023-09-27T07:49:02,954 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert/test-mapseq.hdf5 -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert 2023-09-27T07:49:02,956 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert/test-mapseq.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert 2023-09-27T07:49:02,958 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert/test-mapseq.json -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert 2023-09-27T07:49:02,960 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert 2023-09-27T07:49:02,963 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta 2023-09-27T07:49:02,964 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output 2023-09-27T07:49:02,965 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output/SSU.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output 2023-09-27T07:49:02,967 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output/5S.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output 2023-09-27T07:49:02,969 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output/LSU.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output 2023-09-27T07:49:02,971 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output/prefix_LSU_rRNA_bacteria.RF02541.fa -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output 2023-09-27T07:49:02,973 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output/prefix_SSU_rRNA_bacteria.RF00177.fa -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-output 2023-09-27T07:49:02,974 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/get_subunits.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta 2023-09-27T07:49:02,976 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-input 2023-09-27T07:49:02,977 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-input/test.get_subunits -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/expected-input 2023-09-27T07:49:02,979 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/get_subunits.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta 2023-09-27T07:49:02,981 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta/get_subunits.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/get_subunits_fasta 2023-09-27T07:49:02,983 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch 2023-09-27T07:49:02,984 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/infernal-cmsearch-v1.1.2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch 2023-09-27T07:49:02,986 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/infernal-cmsearch.test.job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch 2023-09-27T07:49:02,989 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input 2023-09-27T07:49:02,990 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input/tRNA5.c.cm -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input 2023-09-27T07:49:02,993 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input/mrum-genome.fa -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input 2023-09-27T07:49:03,040 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input/mt-tmRNA.cm -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/test-input 2023-09-27T07:49:03,044 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/expected_output 2023-09-27T07:49:03,045 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/expected_output/mrum-genome.fa.cmsearch_matches.tbl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/expected_output 2023-09-27T07:49:03,047 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom 2023-09-27T07:49:03,049 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/expected-output 2023-09-27T07:49:03,050 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/expected-output/test-mapseq.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/expected-output 2023-09-27T07:49:03,052 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/expected-output/test.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/expected-output 2023-09-27T07:49:03,054 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/mapseq2biom.pl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom 2023-09-27T07:49:03,056 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/mapseq2biom.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom 2023-09-27T07:49:03,059 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/test-input 2023-09-27T07:49:03,059 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/test-input/test-otu -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/test-input 2023-09-27T07:49:03,062 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/test-input/test-mapseq -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/test-input 2023-09-27T07:49:03,067 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/mapseq2biom-test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom 2023-09-27T07:49:03,069 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/mapseq2biom 2023-09-27T07:49:03,071 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer 2023-09-27T07:49:03,072 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmsearch.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer 2023-09-27T07:49:03,074 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan 2023-09-27T07:49:03,075 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan/hmmscan.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan 2023-09-27T07:49:03,077 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan/chunking-subwf-hmmscan.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan 2023-09-27T07:49:03,079 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan/hmmscan-subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan 2023-09-27T07:49:03,081 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan/hmmscan.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan 2023-09-27T07:49:03,084 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/db 2023-09-27T07:49:03,084 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/db/db_kofam.hmm.h3i -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/db 2023-09-27T07:49:03,097 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification 2023-09-27T07:49:03,098 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/expected-output 2023-09-27T07:49:03,099 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/expected-output/hmmscan_result.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/expected-output 2023-09-27T07:49:03,101 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/hmmscan_tab.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification 2023-09-27T07:49:03,103 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/hmmscan_tab_modification.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification 2023-09-27T07:49:03,105 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/hmmscan_tab_modification.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification 2023-09-27T07:49:03,107 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/test-input 2023-09-27T07:49:03,108 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/test-input/hmmscan_result.tbl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/hmmscan_tab_modification/test-input 2023-09-27T07:49:03,110 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/hmmer 2023-09-27T07:49:03,112 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,113 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/Trimmomatic_PE_test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,115 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic-max_info.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,117 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,119 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic-end_mode.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,120 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/LICENSE -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,123 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic_help.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,125 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/Trimmomatic_SE_test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,127 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic-sliding_window.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,129 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic-phred.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,131 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/Trimmomatic-v0.36-PE.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,134 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/Trimmomatic-v0.36-SE.test.job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,136 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/trimmomatic-illumina_clipping.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,138 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/Trimmomatic-v0.36-SE.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,141 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output 2023-09-27T07:49:03,142 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output/A1_right_ok.fq.trimmed.unpaired.fastq -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output 2023-09-27T07:49:03,143 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output/A1_right_ok.fq.trimmed.fastq -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output 2023-09-27T07:49:03,187 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output/A1_left_ok.fq.trimmed.fastq -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output 2023-09-27T07:49:03,236 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output/A1_left_ok.fq.trimmed.unpaired.fastq -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/expected_output 2023-09-27T07:49:03,238 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic/Trimmomatic-v0.36-PE.test.job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Trimmomatic 2023-09-27T07:49:03,241 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:49:03,242 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/predict_proteins_assemblies.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:49:03,244 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/predict_proteins_assemblies.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:49:03,246 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/predict_proteins_reads.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:49:03,249 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:49:03,250 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.fgs.faa -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:49:03,376 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.prodigal.faa -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:49:03,390 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.fgs.ffn -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:49:03,670 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:49:03,945 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.prodigal.ffn -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:49:03,960 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.prodigal -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:49:03,970 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/ERR3414571_FASTA.cmsearch.all.tblout.deoverlapped -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files 2023-09-27T07:49:03,987 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/prodigal.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:49:03,989 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:49:03,991 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/combined_gene_caller.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:49:03,993 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/combined_gene_caller.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:49:03,995 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/combined_gene_caller_conf.json -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:49:03,997 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/combined_gene_caller.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:49:03,999 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/combined_gene_caller_docker.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:49:04,002 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC 2023-09-27T07:49:04,004 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/FGS.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:49:04,006 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/faselector -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:49:04,008 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/FGS.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:49:04,010 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/unite_protein_predictions.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:49:04,012 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/run_FGS.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:49:04,014 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/post-processing.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller 2023-09-27T07:49:04,016 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly 2023-09-27T07:49:04,017 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Viral 2023-09-27T07:49:04,018 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Viral/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Viral 2023-09-27T07:49:04,021 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis 2023-09-27T07:49:04,022 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/expected-output 2023-09-27T07:49:04,023 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/expected-output/assembly-SRR1620013_small_FASTA_FASTA.summary.kegg_contigs.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/expected-output 2023-09-27T07:49:04,025 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/expected-output/assembly-SRR1620013_small_FASTA_FASTA.summary.kegg_pathways -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/expected-output 2023-09-27T07:49:04,027 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Modification 2023-09-27T07:49:04,028 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Modification/modification_table.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Modification 2023-09-27T07:49:04,030 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Modification/modification_table.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Modification 2023-09-27T07:49:04,032 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan 2023-09-27T07:49:04,033 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan/parsing_hmmscan.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan 2023-09-27T07:49:04,035 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan/parsing_hmmscan.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan 2023-09-27T07:49:04,037 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan/parsing_hmmscan.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan 2023-09-27T07:49:04,039 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker 2023-09-27T07:49:04,040 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker/run_pathways.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker 2023-09-27T07:49:04,042 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker/help_commands.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker 2023-09-27T07:49:04,044 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Docker 2023-09-27T07:49:04,046 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/make_graphs.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis 2023-09-27T07:49:04,048 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways 2023-09-27T07:49:04,049 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways/kegg_pathways.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways 2023-09-27T07:49:04,051 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways/kegg_pathways.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways 2023-09-27T07:49:04,053 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways/give_pathways.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways 2023-09-27T07:49:04,056 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties 2023-09-27T07:49:04,057 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output 2023-09-27T07:49:04,059 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output/LONGFORM_REPORT_test_single_protein.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output 2023-09-27T07:49:04,079 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output/MATCHES_test_single_protein.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output 2023-09-27T07:49:04,080 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output/TABLE_test_single_protein.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output 2023-09-27T07:49:04,092 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output/JSON_test_single_protein.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output 2023-09-27T07:49:04,117 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output/SUMMARY_FILE_test_single_protein.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/expected-output 2023-09-27T07:49:04,121 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/genome_properties.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties 2023-09-27T07:49:04,122 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/genome_properties.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties 2023-09-27T07:49:04,125 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/test-input 2023-09-27T07:49:04,126 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/test-input/InterProScan.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/test-input 2023-09-27T07:49:04,128 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/gp_docker.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties 2023-09-27T07:49:04,129 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Genome_properties 2023-09-27T07:49:04,131 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta 2023-09-27T07:49:04,132 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta/run_samtools.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta 2023-09-27T07:49:04,135 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta/fasta_index.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta 2023-09-27T07:49:04,137 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta/test-input 2023-09-27T07:49:04,139 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta/test-input/test.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta/test-input 2023-09-27T07:49:04,142 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta/fasta_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/index_fasta 2023-09-27T07:49:04,150 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG 2023-09-27T07:49:04,154 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG 2023-09-27T07:49:04,155 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnog.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG 2023-09-27T07:49:04,157 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/emapper.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG 2023-09-27T07:49:04,160 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:49:04,161 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/orthology.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:49:04,163 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/annota.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:49:04,166 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/server.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:49:04,168 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/search.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:49:04,170 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/seqio.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:49:04,172 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/annota_mongo.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:49:04,175 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/vars.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:49:04,179 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/common.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:49:04,181 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:49:04,183 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/version.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:49:04,185 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/utils.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper 2023-09-27T07:49:04,187 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnog.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG 2023-09-27T07:49:04,189 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG 2023-09-27T07:49:04,191 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggnog-subwf.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG 2023-09-27T07:49:04,193 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggnog-subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG 2023-09-27T07:49:04,195 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash 2023-09-27T07:49:04,196 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals 2023-09-27T07:49:04,198 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash_chunking_subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals 2023-09-27T07:49:04,200 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-output 2023-09-27T07:49:04,201 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-output/output-contig-1.gbk -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-output 2023-09-27T07:49:04,224 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-output/output-contig-1.embl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-output 2023-09-27T07:49:04,251 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls 2023-09-27T07:49:04,253 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls/no_antismash_subwf.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls 2023-09-27T07:49:04,256 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls/antismash_subwf.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls 2023-09-27T07:49:04,259 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls/antismash_chunking_subwf.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls 2023-09-27T07:49:04,261 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls/wf_antismash.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/ymls 2023-09-27T07:49:04,265 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing 2023-09-27T07:49:04,267 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/reformat_antismash 2023-09-27T07:49:04,269 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/reformat_antismash/reformat_antismash.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/reformat_antismash 2023-09-27T07:49:04,272 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/reformat_antismash/reformat_antismash.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/reformat_antismash 2023-09-27T07:49:04,276 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk 2023-09-27T07:49:04,277 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk/change_output.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk 2023-09-27T07:49:04,281 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk/change_antismash_output.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk 2023-09-27T07:49:04,285 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk/change_output.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_embl_gbk 2023-09-27T07:49:04,504 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash 2023-09-27T07:49:04,505 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash/antismash_to_gff.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash 2023-09-27T07:49:04,507 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash/antismash_to_gff.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash 2023-09-27T07:49:04,509 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash/antismash_to_gff.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash 2023-09-27T07:49:04,512 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_geneclusters_txt 2023-09-27T07:49:04,513 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_geneclusters_txt/change_geneclusters_txt.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_geneclusters_txt 2023-09-27T07:49:04,515 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_geneclusters_txt/change_geneclusters_ctg.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_geneclusters_txt 2023-09-27T07:49:04,517 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/wf_antismash.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals 2023-09-27T07:49:04,519 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/no_antismash_subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals 2023-09-27T07:49:04,521 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated 2023-09-27T07:49:04,523 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,524 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/after_qc.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,526 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/cmsearch_raw_data.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,528 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/unmapped_from_pfam.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,530 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/pfam_domain_instances.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,532 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/chop_and_avg_for_Pfam2CATH.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,534 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/prepare_reference.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,536 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/functional_annotation_and_post_processing.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,538 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/chop_and_avg_for_CATH2Pfam.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,539 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/run_hmmer.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,541 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/cmsearch_assembly.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,543 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/run_IPS.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,545 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/motus_taxonomy.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,547 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/resmapping_pfam_structs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,549 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/other_ncrnas.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,550 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/run_unite.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,552 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/cath_domain_instances.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,554 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/classify_SSUs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,556 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/unmapped_from_cath.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,558 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/overlap_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,560 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/rna_prediction.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,562 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/chunking_final.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,564 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/avg_unp_domains.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,565 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/run_itsonedb.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,567 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/chop_and_avg_from_list.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,569 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/combined_gene_caller.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,571 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/functional_annotation.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,573 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/trimming.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,574 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/classify_LSUs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,576 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/chop_and_avg_for_core.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,578 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/cgc.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,580 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/resmapping_cath_structs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,581 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/run_manta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,583 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/write_summaries.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,585 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/before_qc.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,587 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/ITS.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,589 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows/find_ribosomal_ncRNAs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/subworkflows 2023-09-27T07:49:04,593 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,594 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/align_avg_structs_pairwise.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,596 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/assign_genes.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,598 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/split_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,600 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/run_rose.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,602 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/counts_to_hdf5.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,604 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/per_unp_dom_instance.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,605 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_lsu_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,607 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/extract_subunits.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,609 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/sam_to_sorted_bam.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,611 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/FGS.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,612 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/rename_png.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,614 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/return_tax_dir.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,616 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/check_alignment_scores.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,618 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/carveme_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,619 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/length_filter.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,621 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/smetana.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,623 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/check_threshold_step.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,625 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/fastqc.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,626 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/samtools_faidx.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,628 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/get_ncrnas.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,630 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/hashsum_paired.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,632 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/return_its_dir.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,634 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/copy_avg_dom.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,635 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/mapseq.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,637 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/memote_run.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,639 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/avg_chopped_structs_unp_domains.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,641 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/reformat_coords.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,642 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,644 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/carveme.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,646 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/tohdt.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,647 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/vcf_compress.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,649 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/ngtax.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,651 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/sort_bed.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,653 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/mask_for_ITS.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,655 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_processed_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,656 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compression.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,658 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/rename_ncrnas.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,660 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/extract_sequences.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,661 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/reduce_bed.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,663 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip_SSU.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,665 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/unzip_merged_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,667 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/manta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,668 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/visualize_otu_counts.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,670 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_cds.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,672 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/return_seq_dir.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,674 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/memote_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,675 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bed_to_macs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,677 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compress_carveme.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,679 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/go_summary.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,681 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/unzip_single_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,683 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/cat_models.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,684 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip_files.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,686 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/make_gff.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,688 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/header_addition.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,690 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/filter_pfam_structures.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,691 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/per_dom_instance.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,693 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/expressiontool_bam_index.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,695 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compress_mapseq.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,697 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/avg_averaged_structures.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,698 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gatk_selectvariants_manta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,700 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip_LSU.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,702 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/make_tab_sep.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,704 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/QC_FLAG.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,705 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compare_instances_CATH_Pfam.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,707 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/conversion.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,709 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chop_structs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,711 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/extract_coords.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,712 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/hashsum_single.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,714 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/pairwise_align_avg_structs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,716 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/format_core_list.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,718 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/picard_create_sequence_dictionary.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,719 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/suppress_tax.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,721 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/post_processing.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,723 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/combine.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,725 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bundle_secondaries.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,726 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/move_to_seq_cat_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,728 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gemstats.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,730 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/touch_no_cds_flag.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,732 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/remove_overlaps.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,733 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/clean_fasta_headers.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,735 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/motus_classification.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,737 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/trim_quality_control.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,739 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/return_output_dir.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,740 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_ITS_seqs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,742 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/move_to_functional_annotation_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,744 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compress.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,745 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/picrust2.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,747 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chunking_tsv.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,749 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/avg_chopped_structures_unp_domains.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,751 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/resmapping_for_Pfam_UP2PDB.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,753 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/interproscan.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,754 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/run_quality_control_filtering.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,756 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/cmsearch.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,758 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gather_domain_like.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,760 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/memote_report_snapshot.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,762 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/run_concatenate_matches.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,764 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gather_failed_domains.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,765 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/touch_empty_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,767 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chinking_fasta_nucleotide.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,769 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/collect_lost_instances.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,771 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/folder_compression.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,773 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/functional_stats.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,774 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_lines_mapseq.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,777 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/rename_manta_samples.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,779 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/crossmapping_CATH2Pfam.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,780 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/overlap_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,782 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/prodigal.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,784 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/add_crossmapped_to_resmapped.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,786 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/convert_trimmed_reads_to_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,787 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/kofamscan.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,789 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bwa_index.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,791 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/reads_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,793 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/filter_cath_structures.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,795 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/pfam.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,796 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/fastqc_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,798 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/run_concatenate_deoverlapped_matches.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,800 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/get_family_ids.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,802 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/no_tax_file_flag.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,803 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chinking_fasta_proteins.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,805 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/ngtax_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,807 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/ngtax_to_tsv_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,809 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_submitted_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,811 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/clean_classification.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,813 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/prodigal_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,815 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/classifications_to_otu_counts.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,817 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/combine_ips.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,819 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_ssu_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,821 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_overlapped_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,822 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/qc_stats.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,824 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/add_domain_positions.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,827 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/combine_trimmed.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,829 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip_masked_ITS.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,831 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/resmapping_for_CATH_PDB2UP.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,833 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/create_new_parameters.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,836 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chinking_SC_fasta_nucleotide.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,838 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/cat.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,841 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/crossmapping_Pfam2CATH.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,843 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/write_summaries.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,846 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_masked_fasta.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,849 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_submitted_reads_single.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,851 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/phyloseq_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,854 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/picrust_files_to_folder.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,856 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/hmmsearch.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,859 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/counts_to_json.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,862 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/avg_averaged_unp_domains.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,864 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/touch_file_flag.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,867 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/index_reads.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,869 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/get_coords.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,872 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compress_prodigal.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,874 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bed_to_bigbed.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,877 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/readmapping_pilon.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,879 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/pilon.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,882 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bam_index.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,885 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/extract_subunits_coords.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,887 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/split_seqs.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,890 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/add_island_names.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,892 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/filter_paired.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,895 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/index_strelka_bed.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules 2023-09-27T07:49:04,898 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/config -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated 2023-09-27T07:49:04,900 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/main.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated 2023-09-27T07:49:04,904 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/filtering_fasta_for_antismash.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals 2023-09-27T07:49:04,907 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/check_value 2023-09-27T07:49:04,908 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/check_value/check_value.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/check_value 2023-09-27T07:49:04,911 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/check_value/check_value.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/check_value 2023-09-27T07:49:04,914 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs 2023-09-27T07:49:04,916 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs/rename_contigs.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs 2023-09-27T07:49:04,918 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs/antismash_rename_contigs.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs 2023-09-27T07:49:04,921 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs/rename_contigs.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/rename_contigs 2023-09-27T07:49:04,924 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:49:04,926 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input/test.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:49:04,929 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input/test.2.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:49:04,932 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input/empty.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:49:04,934 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input/test-1-contig.embl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:49:04,954 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input/test-1-contig.table -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:49:04,955 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input/test.fasta.1 -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/test-input 2023-09-27T07:49:04,957 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash_subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals 2023-09-27T07:49:04,959 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash 2023-09-27T07:49:04,960 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash/antismash_v4.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash 2023-09-27T07:49:04,962 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash/run_antismash_short.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash 2023-09-27T07:49:04,964 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash/antismash_v4.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash 2023-09-27T07:49:04,966 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/move_antismash_summary 2023-09-27T07:49:04,967 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/move_antismash_summary/move_antismash_summary.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/move_antismash_summary 2023-09-27T07:49:04,969 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/move_antismash_summary/move_antismash_summary.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/move_antismash_summary 2023-09-27T07:49:04,972 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:04,973 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.makedb-v0.9.21.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:04,976 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:49:04,978 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_post_run_join.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:49:04,980 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_join.job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:49:04,982 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_join.test.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:49:04,984 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/postprocessing_subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:49:04,986 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_sorting.job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:49:04,987 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_join.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:49:04,989 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_sorting.test.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:49:04,991 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/postprocessing_subwf.test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:49:04,993 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files 2023-09-27T07:49:04,994 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/output_example 2023-09-27T07:49:04,995 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/output_example/example_diamond_10_sorted_join -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/output_example 2023-09-27T07:49:04,997 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/example_diamond_10_sorted -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files 2023-09-27T07:49:04,999 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/example_diamond_db -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files 2023-09-27T07:49:05,001 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/example_diamond_10 -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files 2023-09-27T07:49:05,003 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/postprocessing_subwf.job.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:49:05,004 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_sorting.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:49:05,006 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Dockerfile -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing 2023-09-27T07:49:05,008 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastp-v0.9.21.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:05,010 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastp-v0.9.21_docker.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:05,012 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastp-v0.9.21.test.job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:05,014 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/diamond-subwf.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:05,016 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastx-v0.9.21.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:05,018 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.makedb-v0.9.21.test.job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:05,020 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/diamond-subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:05,022 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-strand_values.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:05,023 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond_blastx_test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:05,025 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-output_formats.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:05,027 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond_blastp_test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:05,029 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastx-v0.9.21.test.job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond 2023-09-27T07:49:05,031 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF 2023-09-27T07:49:05,032 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF/gff_generation.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF 2023-09-27T07:49:05,037 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF/gff_generation.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF 2023-09-27T07:49:05,039 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF/build_assembly_gff.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/GFF 2023-09-27T07:49:05,041 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/SeqPrep 2023-09-27T07:49:05,042 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/SeqPrep/seqprep.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/SeqPrep 2023-09-27T07:49:05,044 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/SeqPrep/seqprep.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/SeqPrep 2023-09-27T07:49:05,046 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows 2023-09-27T07:49:05,047 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls 2023-09-27T07:49:05,048 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls/amplicon-wf--v.5-cond.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls 2023-09-27T07:49:05,051 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls/assembly-pipeline-v.5.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls 2023-09-27T07:49:05,053 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls/raw-reads--v.5-cond.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls 2023-09-27T07:49:05,056 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals 2023-09-27T07:49:05,057 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/assembly 2023-09-27T07:49:05,058 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/assembly/assembly-2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/assembly 2023-09-27T07:49:05,061 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/assembly/assembly-1.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/assembly 2023-09-27T07:49:05,063 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/raw-reads 2023-09-27T07:49:05,064 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/raw-reads/raw-reads-2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/raw-reads 2023-09-27T07:49:05,066 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/raw-reads/raw-reads-1.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/raw-reads 2023-09-27T07:49:05,069 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/amplicon 2023-09-27T07:49:05,070 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/amplicon/amplicon-1.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/amplicon 2023-09-27T07:49:05,072 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/amplicon/amplicon-2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/amplicon 2023-09-27T07:49:05,074 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/out_json_parser.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals 2023-09-27T07:49:05,076 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/README -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals 2023-09-27T07:49:05,078 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/raw-reads-wf--v.5-cond.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows 2023-09-27T07:49:05,082 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:49:05,084 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:49:05,085 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/func_ann_and_post_processing-subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:49:05,089 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/deal_with_functional_annotation.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:49:05,091 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/functional_annotation.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:49:05,094 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/cmsearch-multimodel-assembly.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:49:05,096 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/functional_annotation.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:49:05,098 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/change_formats_and_names.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:49:05,101 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/CGC-subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:49:05,103 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/kegg_analysis.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:49:05,105 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/kegg_analysis.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly 2023-09-27T07:49:05,107 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/seqprep-subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:49:05,110 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/func_summaries.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:49:05,114 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon 2023-09-27T07:49:05,115 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon/ITS-wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon 2023-09-27T07:49:05,118 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon/trim_and_reformat_reads.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon 2023-09-27T07:49:05,120 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon/trimming-not-empty-subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon 2023-09-27T07:49:05,122 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/chunking-subwf-hmmsearch.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:49:05,124 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads 2023-09-27T07:49:05,125 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads/mOTUs-workflow.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads 2023-09-27T07:49:05,127 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads/func_ann_and_post_proccessing-subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads 2023-09-27T07:49:05,129 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads/functional_annotation_raw.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads 2023-09-27T07:49:05,131 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads/CGC-subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads 2023-09-27T07:49:05,133 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/final_chunking.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:49:05,135 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/cmsearch-condition.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:49:05,137 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/cmsearch-multimodel-raw-data.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:49:05,139 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/classify-otu-visualise.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:49:05,140 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/rna_prediction-sub-wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:49:05,143 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/other_ncrnas.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:49:05,145 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/chunking-subwf-IPS.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows 2023-09-27T07:49:05,147 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/assembly-wf--v.5-cond.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows 2023-09-27T07:49:05,149 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/amplicon-wf--v.5-cond.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows 2023-09-27T07:49:05,151 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/profiling 2023-09-27T07:49:05,152 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/profiling/run_profiling.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/profiling 2023-09-27T07:49:05,154 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/profiling/profiling_parser.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/profiling 2023-09-27T07:49:05,156 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,157 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_tab_sep.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,160 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/empty-fasta 2023-09-27T07:49:05,161 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/empty-fasta/empty_fasta.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/empty-fasta 2023-09-27T07:49:05,163 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/empty-fasta/empty_fasta.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/empty-fasta 2023-09-27T07:49:05,165 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta 2023-09-27T07:49:05,165 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta/fastq_to_fasta.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta 2023-09-27T07:49:05,167 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta/fastq_to_fasta.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta 2023-09-27T07:49:05,169 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta/fastq_to_fasta.cwltest.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta 2023-09-27T07:49:05,171 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta/fastq_to_fasta.test.job-input.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastq_to_fasta 2023-09-27T07:49:05,173 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/pigz 2023-09-27T07:49:05,174 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/pigz/gzip.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/pigz 2023-09-27T07:49:05,176 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/test-inputs 2023-09-27T07:49:05,177 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/test-inputs/test_seqs.fq -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/test-inputs 2023-09-27T07:49:05,179 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/test-inputs/test_seqs.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/test-inputs 2023-09-27T07:49:05,182 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header 2023-09-27T07:49:05,182 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header/add_header -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header 2023-09-27T07:49:05,184 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header/add_header.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header 2023-09-27T07:49:05,186 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header/add_header.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/add_header 2023-09-27T07:49:05,188 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_fasta.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,190 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/concatenate.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,191 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/touch_file.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,193 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/qc-flag.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,195 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/clean_fasta_headers.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,197 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines 2023-09-27T07:49:05,198 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines/count_fastq_exp.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines 2023-09-27T07:49:05,200 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines/count_lines.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines 2023-09-27T07:49:05,202 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines/count_lines.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines 2023-09-27T07:49:05,204 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines/count_lines.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_lines 2023-09-27T07:49:05,206 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/return_directory.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,208 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/return_directory.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,211 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/generate_checksum 2023-09-27T07:49:05,212 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/generate_checksum/generate_checksum.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/generate_checksum 2023-09-27T07:49:05,215 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/generate_checksum/generate_checksum.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/generate_checksum 2023-09-27T07:49:05,217 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:49:05,218 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/chunkFastaResultFileUtil.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:49:05,221 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/result_chunker.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:49:05,223 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/run_result_file_chunker.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:49:05,227 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/chunkTSVFileUtil.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:49:05,231 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/cleaningUtils.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:49:05,235 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker 2023-09-27T07:49:05,238 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/move.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,242 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv 2023-09-27T07:49:05,243 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv/make_csv.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv 2023-09-27T07:49:05,246 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv/test.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv 2023-09-27T07:49:05,248 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv/make_csv.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv 2023-09-27T07:49:05,250 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv/output -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv 2023-09-27T07:49:05,252 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/expected_outputs 2023-09-27T07:49:05,253 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/expected_outputs/fasta_chunker 2023-09-27T07:49:05,254 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/expected_outputs/fasta_chunker/test_01_b_test_01_b.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/expected_outputs/fasta_chunker 2023-09-27T07:49:05,256 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/expected_outputs/fasta_chunker/test_02_test_02.fasta -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/expected_outputs/fasta_chunker 2023-09-27T07:49:05,258 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/multiple-gunzip.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,260 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_fasta.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,262 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker 2023-09-27T07:49:05,263 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker/fasta_chunker.test.job.yaml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker 2023-09-27T07:49:05,265 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker/fasta_chunker_test.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker 2023-09-27T07:49:05,266 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker/fasta_chunker.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fasta_chunker 2023-09-27T07:49:05,269 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification 2023-09-27T07:49:05,270 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/expected-output 2023-09-27T07:49:05,271 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/expected-output/hmmscan_result.tsv -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/expected-output 2023-09-27T07:49:05,273 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/hmmscan_tab.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification 2023-09-27T07:49:05,275 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/hmmscan_tab_modification.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification 2023-09-27T07:49:05,277 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/hmmscan_tab_modification.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification 2023-09-27T07:49:05,279 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/test-input 2023-09-27T07:49:05,280 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/test-input/hmmscan_result.tbl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/test-input 2023-09-27T07:49:05,283 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/count_number_lines.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,284 copying build/lib/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/fastp.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils 2023-09-27T07:49:05,287 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows 2023-09-27T07:49:05,288 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,290 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/mark_duplicates_and_sort.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,292 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/bqsr.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,294 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/select_variants.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,295 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/merge_bams.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,297 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/sequence_align_and_tag.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,299 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/apply_bqsr.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,301 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/verify_bam_id.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,303 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/collect_alignment_summary_metrics.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,304 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/collect_hs_metrics.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,306 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/samtools_flagstat.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,308 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/merge_bams_samtools.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,310 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/align_and_tag.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,311 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/name_sort.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,313 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/collect_insert_size_metrics.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,315 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/gatk_haplotype_caller.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,317 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/tools/index_bam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/tools 2023-09-27T07:49:05,319 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/types 2023-09-27T07:49:05,320 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/types/labelled_file.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/types 2023-09-27T07:49:05,322 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/types/trimming_options.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/types 2023-09-27T07:49:05,324 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/types/sequence_data.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/types 2023-09-27T07:49:05,326 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/types/vep_custom_annotation.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/types 2023-09-27T07:49:05,328 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:49:05,329 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/sequence_to_bqsr.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:49:05,331 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/align.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:49:05,332 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/align_sort_markdup.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:49:05,334 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/qc_exome.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:49:05,336 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/sequence_align_and_tag_adapter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:49:05,338 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/hs_metrics.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows 2023-09-27T07:49:05,341 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/pipelines 2023-09-27T07:49:05,342 copying build/lib/janis_core/tests/data/cwl/workflows/analysis-workflows/pipelines/alignment_exome.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/analysis-workflows/pipelines 2023-09-27T07:49:05,345 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:49:05,347 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/ro-crate-preview.html -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:49:05,353 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/CroMaSt.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:49:05,361 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/translated 2023-09-27T07:49:05,364 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/translated/main.nf -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/translated 2023-09-27T07:49:05,369 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/workflow-390-9f3832867eab6c7a6363f8ca594a4bcf2ff7e96f-diagram.svg -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:49:05,374 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/LICENSE -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:49:05,376 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/CONTRIBUTING.md -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:49:05,379 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,379 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/map_unique_struct_cath2pfam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,381 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/other_avg_subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,384 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/separate_cath.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,386 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/download_data.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,388 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/compare_cath_pfam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,390 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/resmapping_pfam2pdb.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,391 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/core_avg_subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,393 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/merge_df2json.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,395 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/crossmapped_per_unp_dom.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,397 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/map_unique_struct_pfam2cath.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,399 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/resmapping_pfam_instances_subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,401 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/gather_lost_resmap.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,403 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/filter_align_scores.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,404 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/add_domain_num.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,406 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/chop_struct2domains.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,408 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/get_family_ids.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,410 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/move_files.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,412 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/align_compute_avg.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,414 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/unmapped_unp_avg_align.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,416 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/pairwise_aligner.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,418 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/list_true_domains.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,421 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,422 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/map_unique_struct_pfam2cath.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,424 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/pairwise_aligner.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,426 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/compare_cath_pfam.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,429 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/separate_cath.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,430 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/separate_pfam.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,433 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/create_param.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,435 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/merge_df2json.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,437 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/add_domain_num.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,438 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/add_crossmapped2resmapped.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,440 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/align_compute_avg.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,443 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/resmapping_cath2up.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,445 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/chop_struct2domains.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,447 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/resmapping_pfam2pdb.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,449 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/map_unique_struct_cath2pfam.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,451 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/residue_mapping.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,453 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/check_threshold.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,456 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/crossmapped_per_unp_dom.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,457 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/filter_align_scores.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,460 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/get_family_ids.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python 2023-09-27T07:49:05,461 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/resmapping_cath_instances_subwf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,464 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/separate_pfam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,466 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/create_param.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,468 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/resmapping_cath2up.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,469 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/add_crossmapped2resmapped.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,471 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/Tools/check_threshold.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/Tools 2023-09-27T07:49:05,473 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/yml 2023-09-27T07:49:05,474 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/yml/download_data.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/yml 2023-09-27T07:49:05,476 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/yml/CroMaSt_input.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/yml 2023-09-27T07:49:05,478 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/yml/environment.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt/yml 2023-09-27T07:49:05,480 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/ro-crate-metadata.json -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:49:05,484 copying build/lib/janis_core/tests/data/cwl/workflows/CroMaSt/README.md -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/CroMaSt 2023-09-27T07:49:05,486 copying build/lib/janis_core/tests/data/cwl/workflows/super_enhancer_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows 2023-09-27T07:49:05,489 copying build/lib/janis_core/tests/data/cwl/workflows/expressions.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows 2023-09-27T07:49:05,491 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/align_sort_markdup 2023-09-27T07:49:05,493 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools 2023-09-27T07:49:05,494 copying build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/mark_duplicates_and_sort.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools 2023-09-27T07:49:05,496 copying build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/merge_bams_samtools.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools 2023-09-27T07:49:05,498 copying build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/align_and_tag.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools 2023-09-27T07:49:05,500 copying build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/name_sort.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools 2023-09-27T07:49:05,502 copying build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/index_bam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/align_sort_markdup/tools 2023-09-27T07:49:05,504 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/align_sort_markdup/subworkflows 2023-09-27T07:49:05,505 copying build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/subworkflows/align.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/align_sort_markdup/subworkflows 2023-09-27T07:49:05,507 copying build/lib/janis_core/tests/data/cwl/workflows/align_sort_markdup/align_sort_markdup.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/align_sort_markdup 2023-09-27T07:49:05,510 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock 2023-09-27T07:49:05,511 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/krona 2023-09-27T07:49:05,513 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/krona/krona.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/krona 2023-09-27T07:49:05,518 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/gtdbtk 2023-09-27T07:49:05,522 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/gtdbtk/gtdbtk_classify_wf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/gtdbtk 2023-09-27T07:49:05,533 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/ena 2023-09-27T07:49:05,535 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/ena/ena_wget.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/ena 2023-09-27T07:49:05,538 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/spades 2023-09-27T07:49:05,538 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/spades/spades.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/spades 2023-09-27T07:49:05,541 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/das_tool 2023-09-27T07:49:05,543 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/das_tool/das_tool.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/das_tool 2023-09-27T07:49:05,548 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/das_tool/fasta_to_contig2bin.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/das_tool 2023-09-27T07:49:05,551 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:49:05,552 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools/merge-sorted-bam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:49:05,554 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools/sam_to_fastq_SE.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:49:05,556 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools/expression_bam_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:49:05,559 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools/sam_to_unmapped_fastq_SE.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:49:05,561 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools/samtools_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:49:05,563 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools/samtools_flagstat.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:49:05,565 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools/samtools_idxstats.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:49:05,567 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools/sam_to_sorted-bam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:49:05,569 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samtools/sam_to_fastq_PE.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/samtools 2023-09-27T07:49:05,571 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/pilon 2023-09-27T07:49:05,572 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/pilon/pilon.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/pilon 2023-09-27T07:49:05,575 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/metagenomics 2023-09-27T07:49:05,576 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metagenomics/get_unbinned_contigs.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/metagenomics 2023-09-27T07:49:05,577 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metagenomics/assembly_bins_readstats.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/metagenomics 2023-09-27T07:49:05,579 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metagenomics/bins_summary.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/metagenomics 2023-09-27T07:49:05,581 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq 2023-09-27T07:49:05,582 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/featurecounts.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq 2023-09-27T07:49:05,585 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/kallisto 2023-09-27T07:49:05,586 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/kallisto/kallisto_quant.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/kallisto 2023-09-27T07:49:05,588 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/kallisto/kallisto_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/kallisto 2023-09-27T07:49:05,590 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/star 2023-09-27T07:49:05,591 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/star/star_align.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/star 2023-09-27T07:49:05,597 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/star/star_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/star 2023-09-27T07:49:05,603 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/.gitkeep -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/RNAseq 2023-09-27T07:49:05,607 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/kraken2 2023-09-27T07:49:05,608 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/kraken2/kraken2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/kraken2 2023-09-27T07:49:05,611 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/kraken2/kraken2-build.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/kraken2 2023-09-27T07:49:05,615 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/clustalo 2023-09-27T07:49:05,618 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/clustalo/clustalo.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/clustalo 2023-09-27T07:49:05,630 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/irods 2023-09-27T07:49:05,633 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/irods/irods_hdt.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/irods 2023-09-27T07:49:05,644 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/irods/irods_manager.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/irods 2023-09-27T07:49:05,656 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/carveme 2023-09-27T07:49:05,660 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/carveme/GEMstats.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/carveme 2023-09-27T07:49:05,670 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/carveme/carveme.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/carveme 2023-09-27T07:49:05,683 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/gunc 2023-09-27T07:49:05,688 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/gunc/gunc.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/gunc 2023-09-27T07:49:05,695 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/semibin 2023-09-27T07:49:05,696 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/semibin/semibin_single_easy_bin.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/semibin 2023-09-27T07:49:05,702 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/semibin/semibin_rename_bins.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/semibin 2023-09-27T07:49:05,708 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/busco 2023-09-27T07:49:05,710 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/busco/busco.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/busco 2023-09-27T07:49:05,717 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/fastp 2023-09-27T07:49:05,719 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/fastp/fastp.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/fastp 2023-09-27T07:49:05,722 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bbmap 2023-09-27T07:49:05,724 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bbmap/bbmap.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bbmap 2023-09-27T07:49:05,729 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bbmap/prepare_fasta_db.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bbmap 2023-09-27T07:49:05,735 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bbmap/bbduk_rrna-filter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bbmap 2023-09-27T07:49:05,740 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bbmap/bbmap_filter-reads.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bbmap 2023-09-27T07:49:05,743 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bbmap/bbduk_filter.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bbmap 2023-09-27T07:49:05,757 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/pycoqc 2023-09-27T07:49:05,764 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/pycoqc/pycoqc.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/pycoqc 2023-09-27T07:49:05,782 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:49:05,787 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp/crt.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:49:05,799 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp/kofamscan.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:49:05,808 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp/infernal.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:49:05,820 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp/interproscan.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:49:05,836 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp/prodigal.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:49:05,845 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp/conversion_rdf2gtf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:49:05,854 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp/toHDT.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:49:05,862 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp/conversion.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:49:05,871 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/sapp/conversion_rdf2fasta.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/sapp 2023-09-27T07:49:05,883 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/metabat2 2023-09-27T07:49:05,887 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metabat2/aggregateBinDepths.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/metabat2 2023-09-27T07:49:05,899 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metabat2/metabatContigDepths.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/metabat2 2023-09-27T07:49:05,903 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/metabat2/metabat2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/metabat2 2023-09-27T07:49:05,906 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/picrust2 2023-09-27T07:49:05,908 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/picrust2/picrust_to_biom.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/picrust2 2023-09-27T07:49:05,911 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/picrust2/picrust2_pipeline.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/picrust2 2023-09-27T07:49:05,915 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/resfinder 2023-09-27T07:49:05,917 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/resfinder/resfinder.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/resfinder 2023-09-27T07:49:05,921 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/multiqc 2023-09-27T07:49:05,923 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/multiqc/multiqc.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/multiqc 2023-09-27T07:49:05,927 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/smetana 2023-09-27T07:49:05,929 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/smetana/smetana.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/smetana 2023-09-27T07:49:05,932 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/longqc 2023-09-27T07:49:05,934 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/longqc/longqc.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/longqc 2023-09-27T07:49:05,938 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/humann 2023-09-27T07:49:05,940 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/humann/humann.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/humann 2023-09-27T07:49:05,943 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/prodigal 2023-09-27T07:49:05,945 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/prodigal/prodigal.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/prodigal 2023-09-27T07:49:05,948 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/samsa2 2023-09-27T07:49:05,950 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/samsa2/convert.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/samsa2 2023-09-27T07:49:05,954 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/eukrep 2023-09-27T07:49:05,955 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/eukrep/eukrep.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/eukrep 2023-09-27T07:49:05,959 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/merge 2023-09-27T07:49:05,960 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/merge/merge.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/merge 2023-09-27T07:49:05,967 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/medaka 2023-09-27T07:49:05,969 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/medaka/medaka.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/medaka 2023-09-27T07:49:05,972 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/medaka/medaka_py.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/medaka 2023-09-27T07:49:05,976 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/minionqc 2023-09-27T07:49:05,978 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/minionqc/minionqc.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/minionqc 2023-09-27T07:49:05,981 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/nanoqc 2023-09-27T07:49:05,983 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/nanoqc/nanoqc.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/nanoqc 2023-09-27T07:49:05,987 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:49:05,988 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows/ngtax_picrust2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:49:05,991 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows/metagenomics_GEM.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:49:05,995 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows/toHDT_compression.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:49:05,998 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows/demultiplexing.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:49:06,001 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows/ngtax.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:49:06,004 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows/sapp_microbes.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:49:06,007 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows/mock_ngtax.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:49:06,010 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/workflows/pilon_mapping.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/workflows 2023-09-27T07:49:06,014 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/minimap2 2023-09-27T07:49:06,016 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/minimap2/minimap2_to_fastq.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/minimap2 2023-09-27T07:49:06,019 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/minimap2/minimap2_to_sorted-bam.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/minimap2 2023-09-27T07:49:06,022 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/minimap2/minimap2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/minimap2 2023-09-27T07:49:06,025 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/aragorn 2023-09-27T07:49:06,027 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/aragorn/aragorn.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/aragorn 2023-09-27T07:49:06,030 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/quast 2023-09-27T07:49:06,032 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/quast/quast.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/quast 2023-09-27T07:49:06,035 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/quast/metaquast.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/quast 2023-09-27T07:49:06,039 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/maxbin2 2023-09-27T07:49:06,040 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/maxbin2/maxbin2.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/maxbin2 2023-09-27T07:49:06,043 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/stats 2023-09-27T07:49:06,044 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/stats/seqinfo.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/stats 2023-09-27T07:49:06,047 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/stats/raw_n50.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/stats 2023-09-27T07:49:06,049 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bowtie2 2023-09-27T07:49:06,051 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bowtie2/bowtie2_index.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bowtie2 2023-09-27T07:49:06,053 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bowtie2/bowtie2_align_simple.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bowtie2 2023-09-27T07:49:06,055 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bowtie2/bowtie2_align.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bowtie2 2023-09-27T07:49:06,059 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/ngtax 2023-09-27T07:49:06,060 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/ngtax/ngtax_to_biom.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/ngtax 2023-09-27T07:49:06,063 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/ngtax/ngtax_to_tsv-fasta.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/ngtax 2023-09-27T07:49:06,066 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/ngtax/ngtax.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/ngtax 2023-09-27T07:49:06,068 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/ngtax/ngtax_demultiplexing.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/ngtax 2023-09-27T07:49:06,070 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:49:06,072 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions/array_to_file.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:49:06,074 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions/files_to_folder.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:49:06,076 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions/merge_dir_arrays.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:49:06,077 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions/folder_file_regex.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:49:06,079 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions/merge_file_arrays.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:49:06,081 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/expressions/folder_to_files.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/expressions 2023-09-27T07:49:06,083 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/fastq 2023-09-27T07:49:06,084 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/fastq/fastq_to_fasta.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/fastq 2023-09-27T07:49:06,086 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/checkm 2023-09-27T07:49:06,087 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/checkm/checkm_lineagewf.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/checkm 2023-09-27T07:49:06,089 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/flye 2023-09-27T07:49:06,090 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/flye/flye.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/flye 2023-09-27T07:49:06,093 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:49:06,094 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash/compress_directory.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:49:06,096 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash/pigz.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:49:06,098 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash/concatenate.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:49:06,099 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash/compress.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:49:06,101 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash/grep_count.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:49:06,103 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash/decompress.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:49:06,105 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/bash/rename.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/bash 2023-09-27T07:49:06,107 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/filtlong 2023-09-27T07:49:06,108 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/filtlong/filtlong.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/filtlong 2023-09-27T07:49:06,111 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,112 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_demultiplexing_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,114 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_GEM_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,117 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_sapp_others_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,120 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_longread_quality_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,123 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_read_annotation_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,128 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_nanopore_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,129 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_samsa2_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,132 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_RNAseq_NonSpliced_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,136 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_sapp_microbes_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,138 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,140 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_assembly_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,149 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_ngtax_picrust2_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,152 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_binning_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,157 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_illumina_assembly_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,161 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_indexbuilder_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,167 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_RNAseq_Spliced_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,172 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_ena_annotation_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,174 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_microbial_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,176 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_illumina_quality_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,180 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_ngtax_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,182 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_pilon_mapping_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,185 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_mock_ngtax_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,187 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_prepare_fasta_db_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,190 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_RNAseq_kallisto_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,194 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_toHDT_compression_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,196 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_genomesync_packed.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/packed 2023-09-27T07:49:06,198 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/memote 2023-09-27T07:49:06,199 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/memote/memote.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/memote 2023-09-27T07:49:06,202 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/guppy 2023-09-27T07:49:06,203 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/guppy/guppy.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/guppy 2023-09-27T07:49:06,205 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/diamond 2023-09-27T07:49:06,206 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/diamond/diamond.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/diamond 2023-09-27T07:49:06,209 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/diamond/view.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/diamond 2023-09-27T07:49:06,211 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/fastqc 2023-09-27T07:49:06,212 copying build/lib/janis_core/tests/data/cwl/workflows/m-unlock/fastqc/fastqc.cwl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/cwl/workflows/m-unlock/fastqc 2023-09-27T07:49:06,215 copying build/lib/janis_core/tests/data/aln.sam -> build/bdist.linux-armv7l/wheel/janis_core/tests/data 2023-09-27T07:49:06,289 copying build/lib/janis_core/tests/data/test.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data 2023-09-27T07:49:06,291 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/wdl 2023-09-27T07:49:06,292 copying build/lib/janis_core/tests/data/wdl/somatic_wf.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/wdl 2023-09-27T07:49:06,295 copying build/lib/janis_core/tests/data/wdl/Multisample_jointgt_GATK4.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/wdl 2023-09-27T07:49:06,298 copying build/lib/janis_core/tests/data/wdl/bwa.wdl -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/wdl 2023-09-27T07:49:06,301 copying build/lib/janis_core/tests/data/mutant_R1.fastq -> build/bdist.linux-armv7l/wheel/janis_core/tests/data 2023-09-27T07:49:06,361 copying build/lib/janis_core/tests/data/wildtype.fna -> build/bdist.linux-armv7l/wheel/janis_core/tests/data 2023-09-27T07:49:06,366 copying build/lib/janis_core/tests/data/test_diff.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data 2023-09-27T07:49:06,368 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,370 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/fastqc-5ec9f6bceaee 2023-09-27T07:49:06,371 copying build/lib/janis_core/tests/data/galaxy/fastqc-5ec9f6bceaee/.hg_archival.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/fastqc-5ec9f6bceaee 2023-09-27T07:49:06,373 copying build/lib/janis_core/tests/data/galaxy/fastqc-5ec9f6bceaee/rgFastQC.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/fastqc-5ec9f6bceaee 2023-09-27T07:49:06,376 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,376 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/.hg_archival.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,378 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/cut.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,381 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/easyjoin -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,383 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/replace_text_in_line.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,385 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/unsorted_uniq.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,387 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/tail.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,389 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/sed.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,391 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/find_and_replace -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,393 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/recurring_lines.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,395 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/multijoin.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,397 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/macros.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,399 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/cat.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,401 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/ansi2html.sh -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,403 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/unfold_column.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,405 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/sort_rows.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,407 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/replace_text_in_column.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,409 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/readme.rst -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,412 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/sort.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,414 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/sort-header -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,416 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/grep.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,418 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/easyjoin.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,420 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/multijoin -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,423 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/head.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,425 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/tac.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,426 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/find_and_replace.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,429 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/sorted_uniq.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,431 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/awk.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,433 copying build/lib/janis_core/tests/data/galaxy/text_processing-d698c222f354/unfold_column.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/text_processing-d698c222f354 2023-09-27T07:49:06,435 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/quast-675488238c96 2023-09-27T07:49:06,436 copying build/lib/janis_core/tests/data/galaxy/quast-675488238c96/macros.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/quast-675488238c96 2023-09-27T07:49:06,438 copying build/lib/janis_core/tests/data/galaxy/quast-675488238c96/quast.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/quast-675488238c96 2023-09-27T07:49:06,441 copying build/lib/janis_core/tests/data/galaxy/goseq_wf.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,443 copying build/lib/janis_core/tests/data/galaxy/rna_seq_counts_to_genes.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,445 copying build/lib/janis_core/tests/data/galaxy/rna_seq_reads_to_counts.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,448 copying build/lib/janis_core/tests/data/galaxy/rna_seq_genes_to_pathways.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,451 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/hisat2-6c19daec423d 2023-09-27T07:49:06,452 copying build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d/.hg_archival.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/hisat2-6c19daec423d 2023-09-27T07:49:06,454 copying build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d/hisat2.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/hisat2-6c19daec423d 2023-09-27T07:49:06,458 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/hisat2-6c19daec423d/tool-data 2023-09-27T07:49:06,459 copying build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d/tool-data/hisat2_indexes.loc.sample -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/hisat2-6c19daec423d/tool-data 2023-09-27T07:49:06,461 copying build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d/tool_data_table_conf.xml.sample -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/hisat2-6c19daec423d 2023-09-27T07:49:06,463 copying build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d/tool_data_table_conf.xml.test -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/hisat2-6c19daec423d 2023-09-27T07:49:06,464 copying build/lib/janis_core/tests/data/galaxy/hisat2-6c19daec423d/hisat2_macros.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/hisat2-6c19daec423d 2023-09-27T07:49:06,466 copying build/lib/janis_core/tests/data/galaxy/cutadapt_wf.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,469 copying build/lib/janis_core/tests/data/galaxy/wf_featurecounts.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,471 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/nanoplot-edbb6c5028f5 2023-09-27T07:49:06,472 copying build/lib/janis_core/tests/data/galaxy/nanoplot-edbb6c5028f5/.hg_archival.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/nanoplot-edbb6c5028f5 2023-09-27T07:49:06,474 copying build/lib/janis_core/tests/data/galaxy/nanoplot-edbb6c5028f5/nanoplot.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/nanoplot-edbb6c5028f5 2023-09-27T07:49:06,476 copying build/lib/janis_core/tests/data/galaxy/unicycler_assembly.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,479 copying build/lib/janis_core/tests/data/galaxy/wf_samtools_idxstats.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,481 copying build/lib/janis_core/tests/data/galaxy/wf_abricate.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,483 copying build/lib/janis_core/tests/data/galaxy/annotate-my-ids-wf.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,484 copying build/lib/janis_core/tests/data/galaxy/wf_mark_duplicates.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,486 copying build/lib/janis_core/tests/data/galaxy/hisat2_wf.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,488 copying build/lib/janis_core/tests/data/galaxy/limma_voom_wf.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,490 copying build/lib/janis_core/tests/data/galaxy/nanoplot_wf.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,493 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate 2023-09-27T07:49:06,494 copying build/lib/janis_core/tests/data/galaxy/abricate/abricate_summary.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate 2023-09-27T07:49:06,496 copying build/lib/janis_core/tests/data/galaxy/abricate/macros.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate 2023-09-27T07:49:06,498 copying build/lib/janis_core/tests/data/galaxy/abricate/.shed.yml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate 2023-09-27T07:49:06,500 creating build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,501 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/MRSA0252.fna -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,555 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/output_summary.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,557 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/test.gbk -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,559 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/output_noresults.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,561 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/output_list.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,563 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/output_mrsa.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,564 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/output_minid100.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,566 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/Acetobacter.fna -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,571 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/output_db-megares.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,574 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/output_noheader.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,576 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/output_db-card.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,579 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/output_mincov100.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,581 copying build/lib/janis_core/tests/data/galaxy/abricate/test-data/output_gbk.txt -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate/test-data 2023-09-27T07:49:06,583 copying build/lib/janis_core/tests/data/galaxy/abricate/abricate.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate 2023-09-27T07:49:06,586 copying build/lib/janis_core/tests/data/galaxy/abricate/abricate_list.xml -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy/abricate 2023-09-27T07:49:06,588 copying build/lib/janis_core/tests/data/galaxy/fastqc_wf.ga -> build/bdist.linux-armv7l/wheel/janis_core/tests/data/galaxy 2023-09-27T07:49:06,591 copying build/lib/janis_core/tests/test_operators.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,594 copying build/lib/janis_core/tests/test_translation_modules.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,597 copying build/lib/janis_core/tests/test_receivefrom.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,599 copying build/lib/janis_core/tests/test_test_runner.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,603 creating build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,604 copying build/lib/janis_core/tests/testworkflows/preprocessing_prune.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,607 copying build/lib/janis_core/tests/testworkflows/components.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,609 copying build/lib/janis_core/tests/testworkflows/plumbing_scatter.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,611 copying build/lib/janis_core/tests/testworkflows/call.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,614 copying build/lib/janis_core/tests/testworkflows/plumbing_type_mismatch.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,616 copying build/lib/janis_core/tests/testworkflows/filenames.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,619 copying build/lib/janis_core/tests/testworkflows/data_sources.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,621 copying build/lib/janis_core/tests/testworkflows/unwrap.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,624 copying build/lib/janis_core/tests/testworkflows/minimal_task_inputs.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,626 copying build/lib/janis_core/tests/testworkflows/all_input_types.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,629 copying build/lib/janis_core/tests/testworkflows/mandatory_types.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,631 copying build/lib/janis_core/tests/testworkflows/naming.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,633 copying build/lib/janis_core/tests/testworkflows/string_formatter.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,635 copying build/lib/janis_core/tests/testworkflows/basics.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,638 copying build/lib/janis_core/tests/testworkflows/subworkflow.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,640 copying build/lib/janis_core/tests/testworkflows/combos.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,642 copying build/lib/janis_core/tests/testworkflows/scatter.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,644 copying build/lib/janis_core/tests/testworkflows/assembly.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,647 copying build/lib/janis_core/tests/testworkflows/plumbing_edge_cases.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,649 copying build/lib/janis_core/tests/testworkflows/trace.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,651 copying build/lib/janis_core/tests/testworkflows/subworkflow2.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,653 copying build/lib/janis_core/tests/testworkflows/process_inputs.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,655 copying build/lib/janis_core/tests/testworkflows/additional_features.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,657 copying build/lib/janis_core/tests/testworkflows/files_directories_to_create.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,659 copying build/lib/janis_core/tests/testworkflows/ordering.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,662 copying build/lib/janis_core/tests/testworkflows/file_pairs.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,665 copying build/lib/janis_core/tests/testworkflows/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,667 copying build/lib/janis_core/tests/testworkflows/optional_types.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,669 copying build/lib/janis_core/tests/testworkflows/outputs.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,672 copying build/lib/janis_core/tests/testworkflows/operations.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,674 copying build/lib/janis_core/tests/testworkflows/duplicate_tasks.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,677 copying build/lib/janis_core/tests/testworkflows/codetools.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,679 copying build/lib/janis_core/tests/testworkflows/secondaries.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,681 copying build/lib/janis_core/tests/testworkflows/script.py -> build/bdist.linux-armv7l/wheel/janis_core/tests/testworkflows 2023-09-27T07:49:06,684 copying build/lib/janis_core/tests/test_metadata.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,686 copying build/lib/janis_core/tests/test_workflow.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,688 copying build/lib/janis_core/tests/test_commandtool.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,690 copying build/lib/janis_core/tests/test_translation_cwl.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,693 copying build/lib/janis_core/tests/tests_util.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,696 copying build/lib/janis_core/tests/test_validators.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,698 copying build/lib/janis_core/tests/test_conditionals.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,700 copying build/lib/janis_core/tests/test_stringbuilder.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,702 copying build/lib/janis_core/tests/test_types.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,705 copying build/lib/janis_core/tests/test_running.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,707 copying build/lib/janis_core/tests/test_ingestion_wdl.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,709 copying build/lib/janis_core/tests/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,711 copying build/lib/janis_core/tests/test_step.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,713 copying build/lib/janis_core/tests/test_ingestion_galaxy.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,716 copying build/lib/janis_core/tests/test_translation_wdl.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,719 copying build/lib/janis_core/tests/test_secondary.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,722 copying build/lib/janis_core/tests/test_python_tool.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,724 copying build/lib/janis_core/tests/test_translation_nextflow.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,729 copying build/lib/janis_core/tests/test_generics_util.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,731 copying build/lib/janis_core/tests/test_ingestion_cwl.py -> build/bdist.linux-armv7l/wheel/janis_core/tests 2023-09-27T07:49:06,734 creating build/bdist.linux-armv7l/wheel/janis_core/settings 2023-09-27T07:49:06,736 creating build/bdist.linux-armv7l/wheel/janis_core/settings/ingest 2023-09-27T07:49:06,737 copying build/lib/janis_core/settings/ingest/cwl.py -> build/bdist.linux-armv7l/wheel/janis_core/settings/ingest 2023-09-27T07:49:06,739 copying build/lib/janis_core/settings/ingest/general.py -> build/bdist.linux-armv7l/wheel/janis_core/settings/ingest 2023-09-27T07:49:06,740 copying build/lib/janis_core/settings/ingest/galaxy.py -> build/bdist.linux-armv7l/wheel/janis_core/settings/ingest 2023-09-27T07:49:06,742 copying build/lib/janis_core/settings/ingest/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/settings/ingest 2023-09-27T07:49:06,744 copying build/lib/janis_core/settings/graph.py -> build/bdist.linux-armv7l/wheel/janis_core/settings 2023-09-27T07:49:06,746 copying build/lib/janis_core/settings/testing.py -> build/bdist.linux-armv7l/wheel/janis_core/settings 2023-09-27T07:49:06,748 creating build/bdist.linux-armv7l/wheel/janis_core/settings/translate 2023-09-27T07:49:06,750 copying build/lib/janis_core/settings/translate/general.py -> build/bdist.linux-armv7l/wheel/janis_core/settings/translate 2023-09-27T07:49:06,752 copying build/lib/janis_core/settings/translate/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/settings/translate 2023-09-27T07:49:06,754 copying build/lib/janis_core/settings/translate/nextflow.py -> build/bdist.linux-armv7l/wheel/janis_core/settings/translate 2023-09-27T07:49:06,756 copying build/lib/janis_core/settings/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/settings 2023-09-27T07:49:06,758 copying build/lib/janis_core/settings/validation.py -> build/bdist.linux-armv7l/wheel/janis_core/settings 2023-09-27T07:49:06,760 copying build/lib/janis_core/settings/datatypes.py -> build/bdist.linux-armv7l/wheel/janis_core/settings 2023-09-27T07:49:06,763 creating build/bdist.linux-armv7l/wheel/janis_core/tool 2023-09-27T07:49:06,764 copying build/lib/janis_core/tool/tool.py -> build/bdist.linux-armv7l/wheel/janis_core/tool 2023-09-27T07:49:06,767 copying build/lib/janis_core/tool/test_suite_runner.py -> build/bdist.linux-armv7l/wheel/janis_core/tool 2023-09-27T07:49:06,770 copying build/lib/janis_core/tool/test_classes.py -> build/bdist.linux-armv7l/wheel/janis_core/tool 2023-09-27T07:49:06,773 copying build/lib/janis_core/tool/test_definitions.py -> build/bdist.linux-armv7l/wheel/janis_core/tool 2023-09-27T07:49:06,776 copying build/lib/janis_core/tool/batchrun.py -> build/bdist.linux-armv7l/wheel/janis_core/tool 2023-09-27T07:49:06,778 copying build/lib/janis_core/tool/cwl_tool_parser.py -> build/bdist.linux-armv7l/wheel/janis_core/tool 2023-09-27T07:49:06,780 copying build/lib/janis_core/tool/documentation.py -> build/bdist.linux-armv7l/wheel/janis_core/tool 2023-09-27T07:49:06,783 copying build/lib/janis_core/tool/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/tool 2023-09-27T07:49:06,785 copying build/lib/janis_core/tool/commandtool.py -> build/bdist.linux-armv7l/wheel/janis_core/tool 2023-09-27T07:49:06,789 copying build/lib/janis_core/tool/test_helpers.py -> build/bdist.linux-armv7l/wheel/janis_core/tool 2023-09-27T07:49:06,793 creating build/bdist.linux-armv7l/wheel/janis_core/hints 2023-09-27T07:49:06,794 copying build/lib/janis_core/hints/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/hints 2023-09-27T07:49:06,797 creating build/bdist.linux-armv7l/wheel/janis_core/translation_deps 2023-09-27T07:49:06,798 copying build/lib/janis_core/translation_deps/exportpath.py -> build/bdist.linux-armv7l/wheel/janis_core/translation_deps 2023-09-27T07:49:06,800 copying build/lib/janis_core/translation_deps/supportedtranslations.py -> build/bdist.linux-armv7l/wheel/janis_core/translation_deps 2023-09-27T07:49:06,803 copying build/lib/janis_core/translation_deps/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translation_deps 2023-09-27T07:49:06,806 creating build/bdist.linux-armv7l/wheel/janis_core/code 2023-09-27T07:49:06,807 copying build/lib/janis_core/code/codetool.py -> build/bdist.linux-armv7l/wheel/janis_core/code 2023-09-27T07:49:06,810 copying build/lib/janis_core/code/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/code 2023-09-27T07:49:06,812 copying build/lib/janis_core/code/pythontool.py -> build/bdist.linux-armv7l/wheel/janis_core/code 2023-09-27T07:49:06,815 creating build/bdist.linux-armv7l/wheel/janis_core/types 2023-09-27T07:49:06,816 copying build/lib/janis_core/types/data_types.py -> build/bdist.linux-armv7l/wheel/janis_core/types 2023-09-27T07:49:06,819 copying build/lib/janis_core/types/common_data_types.py -> build/bdist.linux-armv7l/wheel/janis_core/types 2023-09-27T07:49:06,822 copying build/lib/janis_core/types/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/types 2023-09-27T07:49:06,825 creating build/bdist.linux-armv7l/wheel/janis_core/translation_utils 2023-09-27T07:49:06,826 copying build/lib/janis_core/translation_utils/graph.py -> build/bdist.linux-armv7l/wheel/janis_core/translation_utils 2023-09-27T07:49:06,828 copying build/lib/janis_core/translation_utils/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translation_utils 2023-09-27T07:49:06,830 copying build/lib/janis_core/translation_utils/datatypes.py -> build/bdist.linux-armv7l/wheel/janis_core/translation_utils 2023-09-27T07:49:06,834 creating build/bdist.linux-armv7l/wheel/janis_core/redefinitions 2023-09-27T07:49:06,836 creating build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,837 copying build/lib/janis_core/redefinitions/tools/vcftools.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,840 copying build/lib/janis_core/redefinitions/tools/gatk4.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,845 copying build/lib/janis_core/redefinitions/tools/petermacutils.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,847 copying build/lib/janis_core/redefinitions/tools/bcftools.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,850 copying build/lib/janis_core/redefinitions/tools/fastqc.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,852 copying build/lib/janis_core/redefinitions/tools/gridss.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,855 copying build/lib/janis_core/redefinitions/tools/echo.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,856 copying build/lib/janis_core/redefinitions/tools/uncompressarchive.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,858 copying build/lib/janis_core/redefinitions/tools/bwamem_samtoolsview.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,861 copying build/lib/janis_core/redefinitions/tools/bioinformaticstool.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,863 copying build/lib/janis_core/redefinitions/tools/generate.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,865 copying build/lib/janis_core/redefinitions/tools/performancesummary.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,868 copying build/lib/janis_core/redefinitions/tools/vardict.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,870 copying build/lib/janis_core/redefinitions/tools/splitmultiallele.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,872 copying build/lib/janis_core/redefinitions/tools/manta.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,875 copying build/lib/janis_core/redefinitions/tools/strelka.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,877 copying build/lib/janis_core/redefinitions/tools/addbamstats.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,879 copying build/lib/janis_core/redefinitions/tools/bedtoolsgenomecoverage.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,881 copying build/lib/janis_core/redefinitions/tools/bgzip.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,883 copying build/lib/janis_core/redefinitions/tools/parse.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,886 copying build/lib/janis_core/redefinitions/tools/trimiupac.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,888 copying build/lib/janis_core/redefinitions/tools/cat.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,890 copying build/lib/janis_core/redefinitions/tools/cutadapt.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,892 copying build/lib/janis_core/redefinitions/tools/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,894 copying build/lib/janis_core/redefinitions/tools/tabix.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,896 copying build/lib/janis_core/redefinitions/tools/combinevariants.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,898 copying build/lib/janis_core/redefinitions/tools/samtools.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/tools 2023-09-27T07:49:06,901 copying build/lib/janis_core/redefinitions/types.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions 2023-09-27T07:49:06,905 creating build/bdist.linux-armv7l/wheel/janis_core/redefinitions/workflows 2023-09-27T07:49:06,906 copying build/lib/janis_core/redefinitions/workflows/wgsgermline.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/workflows 2023-09-27T07:49:06,910 copying build/lib/janis_core/redefinitions/workflows/performancesummarygenome.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/workflows 2023-09-27T07:49:06,911 copying build/lib/janis_core/redefinitions/workflows/bwaaligner.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/workflows 2023-09-27T07:49:06,914 copying build/lib/janis_core/redefinitions/workflows/illuminagermlinevariantcaller.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/workflows 2023-09-27T07:49:06,915 copying build/lib/janis_core/redefinitions/workflows/bioinformaticsworkflow.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/workflows 2023-09-27T07:49:06,917 copying build/lib/janis_core/redefinitions/workflows/addbamstats.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/workflows 2023-09-27T07:49:06,919 copying build/lib/janis_core/redefinitions/workflows/vardictgermlinevariantcaller.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/workflows 2023-09-27T07:49:06,921 copying build/lib/janis_core/redefinitions/workflows/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/workflows 2023-09-27T07:49:06,923 copying build/lib/janis_core/redefinitions/workflows/gatkgermlinevariantcaller.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/workflows 2023-09-27T07:49:06,925 copying build/lib/janis_core/redefinitions/workflows/mergeandmark.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/workflows 2023-09-27T07:49:06,927 copying build/lib/janis_core/redefinitions/workflows/gatkbaserecalbqsr.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions/workflows 2023-09-27T07:49:06,929 copying build/lib/janis_core/redefinitions/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions 2023-09-27T07:49:06,930 copying build/lib/janis_core/redefinitions/utils.py -> build/bdist.linux-armv7l/wheel/janis_core/redefinitions 2023-09-27T07:49:06,933 creating build/bdist.linux-armv7l/wheel/janis_core/transformation 2023-09-27T07:49:06,934 copying build/lib/janis_core/transformation/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/transformation 2023-09-27T07:49:06,937 creating build/bdist.linux-armv7l/wheel/janis_core/workflow 2023-09-27T07:49:06,938 copying build/lib/janis_core/workflow/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/workflow 2023-09-27T07:49:06,939 copying build/lib/janis_core/workflow/workflow.py -> build/bdist.linux-armv7l/wheel/janis_core/workflow 2023-09-27T07:49:06,944 creating build/bdist.linux-armv7l/wheel/janis_core/toolbox 2023-09-27T07:49:06,945 copying build/lib/janis_core/toolbox/register.py -> build/bdist.linux-armv7l/wheel/janis_core/toolbox 2023-09-27T07:49:06,947 copying build/lib/janis_core/toolbox/toolbox.py -> build/bdist.linux-armv7l/wheel/janis_core/toolbox 2023-09-27T07:49:06,949 copying build/lib/janis_core/toolbox/entrypoints.py -> build/bdist.linux-armv7l/wheel/janis_core/toolbox 2023-09-27T07:49:06,951 copying build/lib/janis_core/toolbox/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/toolbox 2023-09-27T07:49:06,954 creating build/bdist.linux-armv7l/wheel/janis_core/graph 2023-09-27T07:49:06,955 copying build/lib/janis_core/graph/steptaginput.py -> build/bdist.linux-armv7l/wheel/janis_core/graph 2023-09-27T07:49:06,957 copying build/lib/janis_core/graph/node.py -> build/bdist.linux-armv7l/wheel/janis_core/graph 2023-09-27T07:49:06,959 copying build/lib/janis_core/graph/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/graph 2023-09-27T07:49:06,961 creating build/bdist.linux-armv7l/wheel/janis_core/translations 2023-09-27T07:49:06,962 creating build/bdist.linux-armv7l/wheel/janis_core/translations/janis 2023-09-27T07:49:06,963 copying build/lib/janis_core/translations/janis/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/janis 2023-09-27T07:49:06,966 copying build/lib/janis_core/translations/janis/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/janis 2023-09-27T07:49:06,968 creating build/bdist.linux-armv7l/wheel/janis_core/translations/cwl 2023-09-27T07:49:06,968 copying build/lib/janis_core/translations/cwl/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/cwl 2023-09-27T07:49:06,972 copying build/lib/janis_core/translations/cwl/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/cwl 2023-09-27T07:49:06,974 creating build/bdist.linux-armv7l/wheel/janis_core/translations/common 2023-09-27T07:49:06,975 copying build/lib/janis_core/translations/common/trace.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/common 2023-09-27T07:49:06,978 creating build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing 2023-09-27T07:49:06,979 creating build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing/builders 2023-09-27T07:49:06,980 copying build/lib/janis_core/translations/common/preprocessing/builders/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing/builders 2023-09-27T07:49:06,982 copying build/lib/janis_core/translations/common/preprocessing/builders/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing/builders 2023-09-27T07:49:06,984 creating build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing/prune 2023-09-27T07:49:06,985 copying build/lib/janis_core/translations/common/preprocessing/prune/workflows.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing/prune 2023-09-27T07:49:06,987 copying build/lib/janis_core/translations/common/preprocessing/prune/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing/prune 2023-09-27T07:49:06,989 copying build/lib/janis_core/translations/common/preprocessing/prune/tools.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing/prune 2023-09-27T07:49:06,991 copying build/lib/janis_core/translations/common/preprocessing/prune/gather.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing/prune 2023-09-27T07:49:06,993 copying build/lib/janis_core/translations/common/preprocessing/prune/history.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing/prune 2023-09-27T07:49:06,995 copying build/lib/janis_core/translations/common/preprocessing/prune/common.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing/prune 2023-09-27T07:49:06,997 copying build/lib/janis_core/translations/common/preprocessing/prune/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing/prune 2023-09-27T07:49:06,999 copying build/lib/janis_core/translations/common/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/common/preprocessing 2023-09-27T07:49:07,000 copying build/lib/janis_core/translations/common/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/common 2023-09-27T07:49:07,002 copying build/lib/janis_core/translations/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations 2023-09-27T07:49:07,004 copying build/lib/janis_core/translations/translationbase.py -> build/bdist.linux-armv7l/wheel/janis_core/translations 2023-09-27T07:49:07,008 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow 2023-09-27T07:49:07,008 copying build/lib/janis_core/translations/nextflow/nulls.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow 2023-09-27T07:49:07,010 copying build/lib/janis_core/translations/nextflow/variables.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow 2023-09-27T07:49:07,012 copying build/lib/janis_core/translations/nextflow/expressions.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow 2023-09-27T07:49:07,014 copying build/lib/janis_core/translations/nextflow/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow 2023-09-27T07:49:07,016 copying build/lib/janis_core/translations/nextflow/scope.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow 2023-09-27T07:49:07,018 copying build/lib/janis_core/translations/nextflow/unwrap.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow 2023-09-27T07:49:07,021 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate 2023-09-27T07:49:07,023 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/files 2023-09-27T07:49:07,024 copying build/lib/janis_core/translations/nextflow/generate/files/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/files 2023-09-27T07:49:07,026 copying build/lib/janis_core/translations/nextflow/generate/files/channel_declarations.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/files 2023-09-27T07:49:07,028 copying build/lib/janis_core/translations/nextflow/generate/files/variable_declarations.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/files 2023-09-27T07:49:07,030 copying build/lib/janis_core/translations/nextflow/generate/files/process.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/files 2023-09-27T07:49:07,031 copying build/lib/janis_core/translations/nextflow/generate/files/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/files 2023-09-27T07:49:07,033 copying build/lib/janis_core/translations/nextflow/generate/files/workflow.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/files 2023-09-27T07:49:07,035 copying build/lib/janis_core/translations/nextflow/generate/config.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate 2023-09-27T07:49:07,038 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:49:07,039 copying build/lib/janis_core/translations/nextflow/generate/workflow/call.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:49:07,042 copying build/lib/janis_core/translations/nextflow/generate/workflow/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:49:07,044 copying build/lib/janis_core/translations/nextflow/generate/workflow/scatter.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:49:07,046 copying build/lib/janis_core/translations/nextflow/generate/workflow/edge_cases.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:49:07,048 copying build/lib/janis_core/translations/nextflow/generate/workflow/common.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:49:07,050 copying build/lib/janis_core/translations/nextflow/generate/workflow/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:49:07,051 copying build/lib/janis_core/translations/nextflow/generate/workflow/datatype_mismatch.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/workflow 2023-09-27T07:49:07,054 copying build/lib/janis_core/translations/nextflow/generate/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate 2023-09-27T07:49:07,056 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process 2023-09-27T07:49:07,057 copying build/lib/janis_core/translations/nextflow/generate/process/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process 2023-09-27T07:49:07,059 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/outputs 2023-09-27T07:49:07,060 copying build/lib/janis_core/translations/nextflow/generate/process/outputs/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/outputs 2023-09-27T07:49:07,062 copying build/lib/janis_core/translations/nextflow/generate/process/outputs/factory_cmdtool.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/outputs 2023-09-27T07:49:07,065 copying build/lib/janis_core/translations/nextflow/generate/process/outputs/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/outputs 2023-09-27T07:49:07,067 copying build/lib/janis_core/translations/nextflow/generate/process/outputs/factory_pythontool.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/outputs 2023-09-27T07:49:07,069 copying build/lib/janis_core/translations/nextflow/generate/process/inputs.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process 2023-09-27T07:49:07,072 copying build/lib/janis_core/translations/nextflow/generate/process/directives.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process 2023-09-27T07:49:07,075 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:49:07,076 copying build/lib/janis_core/translations/nextflow/generate/process/script/prescript.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:49:07,079 copying build/lib/janis_core/translations/nextflow/generate/process/script/attributes.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:49:07,080 copying build/lib/janis_core/translations/nextflow/generate/process/script/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:49:07,086 copying build/lib/janis_core/translations/nextflow/generate/process/script/selection.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:49:07,088 copying build/lib/janis_core/translations/nextflow/generate/process/script/ctype.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:49:07,090 copying build/lib/janis_core/translations/nextflow/generate/process/script/ordering.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:49:07,092 copying build/lib/janis_core/translations/nextflow/generate/process/script/common.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:49:07,094 copying build/lib/janis_core/translations/nextflow/generate/process/script/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:49:07,096 copying build/lib/janis_core/translations/nextflow/generate/process/script/script.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process/script 2023-09-27T07:49:07,098 copying build/lib/janis_core/translations/nextflow/generate/process/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/generate/process 2023-09-27T07:49:07,102 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/params 2023-09-27T07:49:07,103 copying build/lib/janis_core/translations/nextflow/params/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/params 2023-09-27T07:49:07,105 copying build/lib/janis_core/translations/nextflow/params/update.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/params 2023-09-27T07:49:07,107 copying build/lib/janis_core/translations/nextflow/params/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/params 2023-09-27T07:49:07,109 copying build/lib/janis_core/translations/nextflow/nfgen_utils.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow 2023-09-27T07:49:07,111 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/preprocessing 2023-09-27T07:49:07,112 copying build/lib/janis_core/translations/nextflow/preprocessing/unique_task_names.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/preprocessing 2023-09-27T07:49:07,114 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:49:07,115 copying build/lib/janis_core/translations/nextflow/preprocessing/task_inputs/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:49:07,117 copying build/lib/janis_core/translations/nextflow/preprocessing/task_inputs/history.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:49:07,119 copying build/lib/janis_core/translations/nextflow/preprocessing/task_inputs/common.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:49:07,122 copying build/lib/janis_core/translations/nextflow/preprocessing/task_inputs/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:49:07,123 copying build/lib/janis_core/translations/nextflow/preprocessing/task_inputs/categories.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:49:07,125 copying build/lib/janis_core/translations/nextflow/preprocessing/task_inputs/populator.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/preprocessing/task_inputs 2023-09-27T07:49:07,127 copying build/lib/janis_core/translations/nextflow/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/preprocessing 2023-09-27T07:49:07,130 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/naming 2023-09-27T07:49:07,131 copying build/lib/janis_core/translations/nextflow/naming/constructs.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/naming 2023-09-27T07:49:07,133 copying build/lib/janis_core/translations/nextflow/naming/process.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/naming 2023-09-27T07:49:07,134 copying build/lib/janis_core/translations/nextflow/naming/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/naming 2023-09-27T07:49:07,137 copying build/lib/janis_core/translations/nextflow/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow 2023-09-27T07:49:07,139 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/casefmt 2023-09-27T07:49:07,140 copying build/lib/janis_core/translations/nextflow/casefmt/mapping.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/casefmt 2023-09-27T07:49:07,142 copying build/lib/janis_core/translations/nextflow/casefmt/patterns.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/casefmt 2023-09-27T07:49:07,144 copying build/lib/janis_core/translations/nextflow/casefmt/casefmt.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/casefmt 2023-09-27T07:49:07,146 copying build/lib/janis_core/translations/nextflow/casefmt/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/casefmt 2023-09-27T07:49:07,147 copying build/lib/janis_core/translations/nextflow/task_inputs.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow 2023-09-27T07:49:07,150 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model 2023-09-27T07:49:07,151 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/files 2023-09-27T07:49:07,152 copying build/lib/janis_core/translations/nextflow/model/files/channels.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/files 2023-09-27T07:49:07,154 copying build/lib/janis_core/translations/nextflow/model/files/variables.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/files 2023-09-27T07:49:07,156 copying build/lib/janis_core/translations/nextflow/model/files/files.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/files 2023-09-27T07:49:07,158 copying build/lib/janis_core/translations/nextflow/model/files/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/files 2023-09-27T07:49:07,160 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/workflow 2023-09-27T07:49:07,161 copying build/lib/janis_core/translations/nextflow/model/workflow/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/workflow 2023-09-27T07:49:07,163 copying build/lib/janis_core/translations/nextflow/model/workflow/workflow.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/workflow 2023-09-27T07:49:07,165 copying build/lib/janis_core/translations/nextflow/model/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model 2023-09-27T07:49:07,167 creating build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/process 2023-09-27T07:49:07,168 copying build/lib/janis_core/translations/nextflow/model/process/process.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/process 2023-09-27T07:49:07,170 copying build/lib/janis_core/translations/nextflow/model/process/inputs.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/process 2023-09-27T07:49:07,172 copying build/lib/janis_core/translations/nextflow/model/process/directives.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/process 2023-09-27T07:49:07,174 copying build/lib/janis_core/translations/nextflow/model/process/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/process 2023-09-27T07:49:07,176 copying build/lib/janis_core/translations/nextflow/model/process/outputs.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/nextflow/model/process 2023-09-27T07:49:07,178 creating build/bdist.linux-armv7l/wheel/janis_core/translations/wdl 2023-09-27T07:49:07,179 copying build/lib/janis_core/translations/wdl/main.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/wdl 2023-09-27T07:49:07,183 copying build/lib/janis_core/translations/wdl/ordering.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/wdl 2023-09-27T07:49:07,185 copying build/lib/janis_core/translations/wdl/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations/wdl 2023-09-27T07:49:07,186 copying build/lib/janis_core/translations/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/translations 2023-09-27T07:49:07,188 copying build/lib/janis_core/__meta__.py -> build/bdist.linux-armv7l/wheel/janis_core 2023-09-27T07:49:07,190 copying build/lib/janis_core/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core 2023-09-27T07:49:07,193 creating build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,194 copying build/lib/janis_core/utils/metadata.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,195 copying build/lib/janis_core/utils/bracketmatching.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,197 copying build/lib/janis_core/utils/pickvalue.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,199 copying build/lib/janis_core/utils/errors.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,201 copying build/lib/janis_core/utils/levenshteindistance.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,203 copying build/lib/janis_core/utils/docparser_info.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,205 copying build/lib/janis_core/utils/scatter.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,207 copying build/lib/janis_core/utils/secondary.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,209 copying build/lib/janis_core/utils/generators.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,212 copying build/lib/janis_core/utils/yaml_utils.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,213 copying build/lib/janis_core/utils/janisconstants.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,215 copying build/lib/janis_core/utils/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,217 copying build/lib/janis_core/utils/logger.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,219 copying build/lib/janis_core/utils/validators.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,220 copying build/lib/janis_core/utils/generics_util.py -> build/bdist.linux-armv7l/wheel/janis_core/utils 2023-09-27T07:49:07,223 creating build/bdist.linux-armv7l/wheel/janis_core/messages 2023-09-27T07:49:07,224 copying build/lib/janis_core/messages/main.py -> build/bdist.linux-armv7l/wheel/janis_core/messages 2023-09-27T07:49:07,226 copying build/lib/janis_core/messages/config.yaml -> build/bdist.linux-armv7l/wheel/janis_core/messages 2023-09-27T07:49:07,227 copying build/lib/janis_core/messages/logfile.py -> build/bdist.linux-armv7l/wheel/janis_core/messages 2023-09-27T07:49:07,229 copying build/lib/janis_core/messages/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/messages 2023-09-27T07:49:07,231 creating build/bdist.linux-armv7l/wheel/janis_core/operators 2023-09-27T07:49:07,232 copying build/lib/janis_core/operators/selectors.py -> build/bdist.linux-armv7l/wheel/janis_core/operators 2023-09-27T07:49:07,235 copying build/lib/janis_core/operators/logical.py -> build/bdist.linux-armv7l/wheel/janis_core/operators 2023-09-27T07:49:07,237 copying build/lib/janis_core/operators/operator.py -> build/bdist.linux-armv7l/wheel/janis_core/operators 2023-09-27T07:49:07,239 copying build/lib/janis_core/operators/standard.py -> build/bdist.linux-armv7l/wheel/janis_core/operators 2023-09-27T07:49:07,242 copying build/lib/janis_core/operators/__init__.py -> build/bdist.linux-armv7l/wheel/janis_core/operators 2023-09-27T07:49:07,266 copying build/lib/janis_core/operators/stringformatter.py -> build/bdist.linux-armv7l/wheel/janis_core/operators 2023-09-27T07:49:07,268 running install_egg_info 2023-09-27T07:49:07,273 Copying janis_pipelines.core.egg-info to build/bdist.linux-armv7l/wheel/janis_pipelines.core-0.13.1-py3.11.egg-info 2023-09-27T07:49:07,288 running install_scripts 2023-09-27T07:49:07,313 creating build/bdist.linux-armv7l/wheel/janis_pipelines.core-0.13.1.dist-info/WHEEL 2023-09-27T07:49:07,315 creating '/tmp/pip-wheel-bvvu18yt/.tmp-gwuc1q_9/janis_pipelines.core-0.13.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-27T07:49:07,318 adding 'janis_core/__init__.py' 2023-09-27T07:49:07,319 adding 'janis_core/__meta__.py' 2023-09-27T07:49:07,321 adding 'janis_core/code/__init__.py' 2023-09-27T07:49:07,322 adding 'janis_core/code/codetool.py' 2023-09-27T07:49:07,324 adding 'janis_core/code/pythontool.py' 2023-09-27T07:49:07,326 adding 'janis_core/graph/__init__.py' 2023-09-27T07:49:07,327 adding 'janis_core/graph/node.py' 2023-09-27T07:49:07,329 adding 'janis_core/graph/steptaginput.py' 2023-09-27T07:49:07,331 adding 'janis_core/hints/__init__.py' 2023-09-27T07:49:07,332 adding 'janis_core/ingestion/SupportedIngestion.py' 2023-09-27T07:49:07,334 adding 'janis_core/ingestion/__init__.py' 2023-09-27T07:49:07,335 adding 'janis_core/ingestion/main.py' 2023-09-27T07:49:07,336 adding 'janis_core/ingestion/cwl/__init__.py' 2023-09-27T07:49:07,338 adding 'janis_core/ingestion/cwl/expressions.py' 2023-09-27T07:49:07,339 adding 'janis_core/ingestion/cwl/graph.py' 2023-09-27T07:49:07,340 adding 'janis_core/ingestion/cwl/identifiers.py' 2023-09-27T07:49:07,342 adding 'janis_core/ingestion/cwl/loading.py' 2023-09-27T07:49:07,343 adding 'janis_core/ingestion/cwl/main.py' 2023-09-27T07:49:07,345 adding 'janis_core/ingestion/cwl/preprocessing.py' 2023-09-27T07:49:07,347 adding 'janis_core/ingestion/cwl/types.py' 2023-09-27T07:49:07,348 adding 'janis_core/ingestion/cwl/parsing/__init__.py' 2023-09-27T07:49:07,352 adding 'janis_core/ingestion/cwl/parsing/tool.py' 2023-09-27T07:49:07,353 adding 'janis_core/ingestion/cwl/parsing/workflow.py' 2023-09-27T07:49:07,360 adding 'janis_core/ingestion/data/janis_types.yaml' 2023-09-27T07:49:07,362 adding 'janis_core/ingestion/data/logging_config.yaml' 2023-09-27T07:49:07,370 adding 'janis_core/ingestion/data/galaxy/datatypes_conf.xml.sample' 2023-09-27T07:49:07,372 adding 'janis_core/ingestion/data/galaxy/galaxy_config.yaml' 2023-09-27T07:49:07,374 adding 'janis_core/ingestion/galaxy/__init__.py' 2023-09-27T07:49:07,375 adding 'janis_core/ingestion/galaxy/aliases.py' 2023-09-27T07:49:07,376 adding 'janis_core/ingestion/galaxy/ingest.py' 2023-09-27T07:49:07,378 adding 'janis_core/ingestion/galaxy/logging.py' 2023-09-27T07:49:07,380 adding 'janis_core/ingestion/galaxy/containers/Container.py' 2023-09-27T07:49:07,381 adding 'janis_core/ingestion/galaxy/containers/__init__.py' 2023-09-27T07:49:07,382 adding 'janis_core/ingestion/galaxy/containers/cache.py' 2023-09-27T07:49:07,383 adding 'janis_core/ingestion/galaxy/containers/fetch.py' 2023-09-27T07:49:07,385 adding 'janis_core/ingestion/galaxy/containers/main.py' 2023-09-27T07:49:07,386 adding 'janis_core/ingestion/galaxy/containers/mulled.py' 2023-09-27T07:49:07,388 adding 'janis_core/ingestion/galaxy/containers/fetching/ContainerReqFetcher.py' 2023-09-27T07:49:07,390 adding 'janis_core/ingestion/galaxy/containers/fetching/Fetcher.py' 2023-09-27T07:49:07,391 adding 'janis_core/ingestion/galaxy/containers/fetching/GA4GHFetcher.py' 2023-09-27T07:49:07,392 adding 'janis_core/ingestion/galaxy/containers/fetching/QuayIOFetcher.py' 2023-09-27T07:49:07,393 adding 'janis_core/ingestion/galaxy/containers/fetching/__init__.py' 2023-09-27T07:49:07,395 adding 'janis_core/ingestion/galaxy/containers/fetching/presets.py' 2023-09-27T07:49:07,396 adding 'janis_core/ingestion/galaxy/containers/fetching/utils.py' 2023-09-27T07:49:07,398 adding 'janis_core/ingestion/galaxy/containers/selection/VersionMatcher.py' 2023-09-27T07:49:07,399 adding 'janis_core/ingestion/galaxy/containers/selection/__init__.py' 2023-09-27T07:49:07,400 adding 'janis_core/ingestion/galaxy/containers/selection/selection.py' 2023-09-27T07:49:07,402 adding 'janis_core/ingestion/galaxy/datatypes/JanisDatatype.py' 2023-09-27T07:49:07,403 adding 'janis_core/ingestion/galaxy/datatypes/__init__.py' 2023-09-27T07:49:07,404 adding 'janis_core/ingestion/galaxy/datatypes/conversion.py' 2023-09-27T07:49:07,406 adding 'janis_core/ingestion/galaxy/datatypes/core.py' 2023-09-27T07:49:07,413 adding 'janis_core/ingestion/galaxy/datatypes/galaxy.py' 2023-09-27T07:49:07,419 adding 'janis_core/ingestion/galaxy/datatypes/main.py' 2023-09-27T07:49:07,424 adding 'janis_core/ingestion/galaxy/datatypes/register.py' 2023-09-27T07:49:07,429 adding 'janis_core/ingestion/galaxy/datatypes/strategies.py' 2023-09-27T07:49:07,458 adding 'janis_core/ingestion/galaxy/expressions/__init__.py' 2023-09-27T07:49:07,459 adding 'janis_core/ingestion/galaxy/expressions/checks.py' 2023-09-27T07:49:07,460 adding 'janis_core/ingestion/galaxy/expressions/matches.py' 2023-09-27T07:49:07,462 adding 'janis_core/ingestion/galaxy/expressions/patterns.py' 2023-09-27T07:49:07,464 adding 'janis_core/ingestion/galaxy/fileio/__init__.py' 2023-09-27T07:49:07,465 adding 'janis_core/ingestion/galaxy/fileio/initialisation.py' 2023-09-27T07:49:07,466 adding 'janis_core/ingestion/galaxy/fileio/write.py' 2023-09-27T07:49:07,467 adding 'janis_core/ingestion/galaxy/fileio/formats/DefaultFormat.py' 2023-09-27T07:49:07,469 adding 'janis_core/ingestion/galaxy/fileio/formats/Format.py' 2023-09-27T07:49:07,470 adding 'janis_core/ingestion/galaxy/fileio/formats/SubworkflowFormat.py' 2023-09-27T07:49:07,471 adding 'janis_core/ingestion/galaxy/fileio/formats/__init__.py' 2023-09-27T07:49:07,472 adding 'janis_core/ingestion/galaxy/fileio/text/TextRender.py' 2023-09-27T07:49:07,473 adding 'janis_core/ingestion/galaxy/fileio/text/__init__.py' 2023-09-27T07:49:07,475 adding 'janis_core/ingestion/galaxy/fileio/text/formatting.py' 2023-09-27T07:49:07,476 adding 'janis_core/ingestion/galaxy/fileio/text/ordering.py' 2023-09-27T07:49:07,478 adding 'janis_core/ingestion/galaxy/fileio/text/tool/ConfigfileText.py' 2023-09-27T07:49:07,479 adding 'janis_core/ingestion/galaxy/fileio/text/tool/ToolInputSectionText.py' 2023-09-27T07:49:07,480 adding 'janis_core/ingestion/galaxy/fileio/text/tool/ToolInputText.py' 2023-09-27T07:49:07,482 adding 'janis_core/ingestion/galaxy/fileio/text/tool/ToolOutputSectionText.py' 2023-09-27T07:49:07,483 adding 'janis_core/ingestion/galaxy/fileio/text/tool/ToolOutputText.py' 2023-09-27T07:49:07,484 adding 'janis_core/ingestion/galaxy/fileio/text/tool/ToolText.py' 2023-09-27T07:49:07,486 adding 'janis_core/ingestion/galaxy/fileio/text/tool/UnstranslatedText.py' 2023-09-27T07:49:07,487 adding 'janis_core/ingestion/galaxy/fileio/text/tool/__init__.py' 2023-09-27T07:49:07,489 adding 'janis_core/ingestion/galaxy/fileio/text/workflow/ConfigText.py' 2023-09-27T07:49:07,491 adding 'janis_core/ingestion/galaxy/fileio/text/workflow/InputsText.py' 2023-09-27T07:49:07,492 adding 'janis_core/ingestion/galaxy/fileio/text/workflow/StepText.py' 2023-09-27T07:49:07,494 adding 'janis_core/ingestion/galaxy/fileio/text/workflow/WorkflowInputText.py' 2023-09-27T07:49:07,495 adding 'janis_core/ingestion/galaxy/fileio/text/workflow/WorkflowOutputText.py' 2023-09-27T07:49:07,496 adding 'janis_core/ingestion/galaxy/fileio/text/workflow/WorkflowText.py' 2023-09-27T07:49:07,497 adding 'janis_core/ingestion/galaxy/fileio/text/workflow/__init__.py' 2023-09-27T07:49:07,499 adding 'janis_core/ingestion/galaxy/gxtool/TestRegister.py' 2023-09-27T07:49:07,500 adding 'janis_core/ingestion/galaxy/gxtool/__init__.py' 2023-09-27T07:49:07,502 adding 'janis_core/ingestion/galaxy/gxtool/mock.py' 2023-09-27T07:49:07,505 adding 'janis_core/ingestion/galaxy/gxtool/command/Command.py' 2023-09-27T07:49:07,506 adding 'janis_core/ingestion/galaxy/gxtool/command/__init__.py' 2023-09-27T07:49:07,509 adding 'janis_core/ingestion/galaxy/gxtool/command/annotation.py' 2023-09-27T07:49:07,510 adding 'janis_core/ingestion/galaxy/gxtool/command/epaths.py' 2023-09-27T07:49:07,511 adding 'janis_core/ingestion/galaxy/gxtool/command/loading.py' 2023-09-27T07:49:07,513 adding 'janis_core/ingestion/galaxy/gxtool/command/main.py' 2023-09-27T07:49:07,514 adding 'janis_core/ingestion/galaxy/gxtool/command/tokenise.py' 2023-09-27T07:49:07,516 adding 'janis_core/ingestion/galaxy/gxtool/command/update.py' 2023-09-27T07:49:07,517 adding 'janis_core/ingestion/galaxy/gxtool/command/cmdstr/CommandString.py' 2023-09-27T07:49:07,519 adding 'janis_core/ingestion/galaxy/gxtool/command/cmdstr/DynamicCommandStatement.py' 2023-09-27T07:49:07,520 adding 'janis_core/ingestion/galaxy/gxtool/command/cmdstr/MainStatementInferrer.py' 2023-09-27T07:49:07,522 adding 'janis_core/ingestion/galaxy/gxtool/command/cmdstr/RealisedTokenValues.py' 2023-09-27T07:49:07,523 adding 'janis_core/ingestion/galaxy/gxtool/command/cmdstr/__init__.py' 2023-09-27T07:49:07,524 adding 'janis_core/ingestion/galaxy/gxtool/command/cmdstr/analysis.py' 2023-09-27T07:49:07,526 adding 'janis_core/ingestion/galaxy/gxtool/command/cmdstr/constructs.py' 2023-09-27T07:49:07,527 adding 'janis_core/ingestion/galaxy/gxtool/command/cmdstr/generate.py' 2023-09-27T07:49:07,528 adding 'janis_core/ingestion/galaxy/gxtool/command/cmdstr/utils.py' 2023-09-27T07:49:07,531 adding 'janis_core/ingestion/galaxy/gxtool/command/components/CommandComponent.py' 2023-09-27T07:49:07,532 adding 'janis_core/ingestion/galaxy/gxtool/command/components/ValueRecord.py' 2023-09-27T07:49:07,533 adding 'janis_core/ingestion/galaxy/gxtool/command/components/__init__.py' 2023-09-27T07:49:07,535 adding 'janis_core/ingestion/galaxy/gxtool/command/components/factory.py' 2023-09-27T07:49:07,536 adding 'janis_core/ingestion/galaxy/gxtool/command/components/inputs/Flag.py' 2023-09-27T07:49:07,538 adding 'janis_core/ingestion/galaxy/gxtool/command/components/inputs/InputComponent.py' 2023-09-27T07:49:07,539 adding 'janis_core/ingestion/galaxy/gxtool/command/components/inputs/Option.py' 2023-09-27T07:49:07,540 adding 'janis_core/ingestion/galaxy/gxtool/command/components/inputs/Positional.py' 2023-09-27T07:49:07,542 adding 'janis_core/ingestion/galaxy/gxtool/command/components/inputs/__init__.py' 2023-09-27T07:49:07,543 adding 'janis_core/ingestion/galaxy/gxtool/command/components/inputs/utils.py' 2023-09-27T07:49:07,545 adding 'janis_core/ingestion/galaxy/gxtool/command/components/linux/Tee.py' 2023-09-27T07:49:07,546 adding 'janis_core/ingestion/galaxy/gxtool/command/components/linux/__init__.py' 2023-09-27T07:49:07,547 adding 'janis_core/ingestion/galaxy/gxtool/command/components/linux/streams.py' 2023-09-27T07:49:07,548 adding 'janis_core/ingestion/galaxy/gxtool/command/components/outputs/InputOutput.py' 2023-09-27T07:49:07,550 adding 'janis_core/ingestion/galaxy/gxtool/command/components/outputs/OutputComponent.py' 2023-09-27T07:49:07,551 adding 'janis_core/ingestion/galaxy/gxtool/command/components/outputs/RedirectOutput.py' 2023-09-27T07:49:07,553 adding 'janis_core/ingestion/galaxy/gxtool/command/components/outputs/WildcardOutput.py' 2023-09-27T07:49:07,554 adding 'janis_core/ingestion/galaxy/gxtool/command/components/outputs/__init__.py' 2023-09-27T07:49:07,557 adding 'janis_core/ingestion/galaxy/gxtool/command/epath/Annotator.py' 2023-09-27T07:49:07,559 adding 'janis_core/ingestion/galaxy/gxtool/command/epath/ComponentOrderingStrategy.py' 2023-09-27T07:49:07,560 adding 'janis_core/ingestion/galaxy/gxtool/command/epath/ExecutionPath.py' 2023-09-27T07:49:07,563 adding 'janis_core/ingestion/galaxy/gxtool/command/epath/ExecutionPathAnnotator.py' 2023-09-27T07:49:07,564 adding 'janis_core/ingestion/galaxy/gxtool/command/epath/__init__.py' 2023-09-27T07:49:07,566 adding 'janis_core/ingestion/galaxy/gxtool/command/epath/analysis.py' 2023-09-27T07:49:07,569 adding 'janis_core/ingestion/galaxy/gxtool/command/tokens/__init__.py' 2023-09-27T07:49:07,571 adding 'janis_core/ingestion/galaxy/gxtool/command/tokens/factory.py' 2023-09-27T07:49:07,573 adding 'janis_core/ingestion/galaxy/gxtool/command/tokens/prioritisation.py' 2023-09-27T07:49:07,575 adding 'janis_core/ingestion/galaxy/gxtool/command/tokens/token.py' 2023-09-27T07:49:07,577 adding 'janis_core/ingestion/galaxy/gxtool/command/tokens/utils.py' 2023-09-27T07:49:07,579 adding 'janis_core/ingestion/galaxy/gxtool/model/__init__.py' 2023-09-27T07:49:07,581 adding 'janis_core/ingestion/galaxy/gxtool/model/citations.py' 2023-09-27T07:49:07,582 adding 'janis_core/ingestion/galaxy/gxtool/model/configfile.py' 2023-09-27T07:49:07,584 adding 'janis_core/ingestion/galaxy/gxtool/model/metadata.py' 2023-09-27T07:49:07,586 adding 'janis_core/ingestion/galaxy/gxtool/model/requirement.py' 2023-09-27T07:49:07,588 adding 'janis_core/ingestion/galaxy/gxtool/model/script.py' 2023-09-27T07:49:07,589 adding 'janis_core/ingestion/galaxy/gxtool/model/tests.py' 2023-09-27T07:49:07,591 adding 'janis_core/ingestion/galaxy/gxtool/model/tool.py' 2023-09-27T07:49:07,593 adding 'janis_core/ingestion/galaxy/gxtool/model/params/__init__.py' 2023-09-27T07:49:07,595 adding 'janis_core/ingestion/galaxy/gxtool/model/params/input_param.py' 2023-09-27T07:49:07,597 adding 'janis_core/ingestion/galaxy/gxtool/model/params/output_param.py' 2023-09-27T07:49:07,599 adding 'janis_core/ingestion/galaxy/gxtool/model/params/param.py' 2023-09-27T07:49:07,601 adding 'janis_core/ingestion/galaxy/gxtool/model/params/param_register.py' 2023-09-27T07:49:07,603 adding 'janis_core/ingestion/galaxy/gxtool/parsing/__init__.py' 2023-09-27T07:49:07,605 adding 'janis_core/ingestion/galaxy/gxtool/parsing/inputs.py' 2023-09-27T07:49:07,608 adding 'janis_core/ingestion/galaxy/gxtool/parsing/main.py' 2023-09-27T07:49:07,610 adding 'janis_core/ingestion/galaxy/gxtool/parsing/outputs.py' 2023-09-27T07:49:07,612 adding 'janis_core/ingestion/galaxy/gxtool/parsing/param_flattener.py' 2023-09-27T07:49:07,615 adding 'janis_core/ingestion/galaxy/gxtool/parsing/tests/TestFactoryOld.py' 2023-09-27T07:49:07,617 adding 'janis_core/ingestion/galaxy/gxtool/parsing/tests/__init__.py' 2023-09-27T07:49:07,619 adding 'janis_core/ingestion/galaxy/gxtool/parsing/tests/checks.py' 2023-09-27T07:49:07,620 adding 'janis_core/ingestion/galaxy/gxtool/parsing/tests/custom_ops.py' 2023-09-27T07:49:07,622 adding 'janis_core/ingestion/galaxy/gxtool/parsing/tests/custom_preprocessors.py' 2023-09-27T07:49:07,624 adding 'janis_core/ingestion/galaxy/gxtool/parsing/tests/mapper.py' 2023-09-27T07:49:07,626 adding 'janis_core/ingestion/galaxy/gxtool/text/__init__.py' 2023-09-27T07:49:07,627 adding 'janis_core/ingestion/galaxy/gxtool/text/utils.py' 2023-09-27T07:49:07,629 adding 'janis_core/ingestion/galaxy/gxtool/text/cheetah/__init__.py' 2023-09-27T07:49:07,633 adding 'janis_core/ingestion/galaxy/gxtool/text/cheetah/blocks.py' 2023-09-27T07:49:07,635 adding 'janis_core/ingestion/galaxy/gxtool/text/cheetah/evaluation.py' 2023-09-27T07:49:07,638 adding 'janis_core/ingestion/galaxy/gxtool/text/simplification/__init__.py' 2023-09-27T07:49:07,640 adding 'janis_core/ingestion/galaxy/gxtool/text/simplification/aliases.py' 2023-09-27T07:49:07,642 adding 'janis_core/ingestion/galaxy/gxtool/text/simplification/filters.py' 2023-09-27T07:49:07,644 adding 'janis_core/ingestion/galaxy/gxtool/text/simplification/main_statement.py' 2023-09-27T07:49:07,646 adding 'janis_core/ingestion/galaxy/gxtool/text/simplification/simplify.py' 2023-09-27T07:49:07,648 adding 'janis_core/ingestion/galaxy/gxworkflow/__init__.py' 2023-09-27T07:49:07,650 adding 'janis_core/ingestion/galaxy/gxworkflow/connections/__init__.py' 2023-09-27T07:49:07,652 adding 'janis_core/ingestion/galaxy/gxworkflow/connections/scatter.py' 2023-09-27T07:49:07,654 adding 'janis_core/ingestion/galaxy/gxworkflow/parsing/__init__.py' 2023-09-27T07:49:07,655 adding 'janis_core/ingestion/galaxy/gxworkflow/parsing/inputs.py' 2023-09-27T07:49:07,656 adding 'janis_core/ingestion/galaxy/gxworkflow/parsing/metadata.py' 2023-09-27T07:49:07,658 adding 'janis_core/ingestion/galaxy/gxworkflow/parsing/step.py' 2023-09-27T07:49:07,659 adding 'janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/__init__.py' 2023-09-27T07:49:07,660 adding 'janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/metadata.py' 2023-09-27T07:49:07,662 adding 'janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/outputs.py' 2023-09-27T07:49:07,663 adding 'janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/prepost.py' 2023-09-27T07:49:07,664 adding 'janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/tool.py' 2023-09-27T07:49:07,666 adding 'janis_core/ingestion/galaxy/gxworkflow/tool_state/__init__.py' 2023-09-27T07:49:07,667 adding 'janis_core/ingestion/galaxy/gxworkflow/tool_state/filters.py' 2023-09-27T07:49:07,669 adding 'janis_core/ingestion/galaxy/gxworkflow/tool_state/load.py' 2023-09-27T07:49:07,670 adding 'janis_core/ingestion/galaxy/gxworkflow/updates/__init__.py' 2023-09-27T07:49:07,672 adding 'janis_core/ingestion/galaxy/gxworkflow/updates/arrays.py' 2023-09-27T07:49:07,673 adding 'janis_core/ingestion/galaxy/gxworkflow/updates/datatypes.py' 2023-09-27T07:49:07,674 adding 'janis_core/ingestion/galaxy/gxworkflow/updates/main.py' 2023-09-27T07:49:07,675 adding 'janis_core/ingestion/galaxy/gxworkflow/updates/optionality.py' 2023-09-27T07:49:07,677 adding 'janis_core/ingestion/galaxy/gxworkflow/values/__init__.py' 2023-09-27T07:49:07,678 adding 'janis_core/ingestion/galaxy/gxworkflow/values/connection.py' 2023-09-27T07:49:07,679 adding 'janis_core/ingestion/galaxy/gxworkflow/values/default.py' 2023-09-27T07:49:07,680 adding 'janis_core/ingestion/galaxy/gxworkflow/values/factory.py' 2023-09-27T07:49:07,682 adding 'janis_core/ingestion/galaxy/gxworkflow/values/runtime.py' 2023-09-27T07:49:07,683 adding 'janis_core/ingestion/galaxy/gxworkflow/values/scripts.py' 2023-09-27T07:49:07,685 adding 'janis_core/ingestion/galaxy/gxworkflow/values/static.py' 2023-09-27T07:49:07,686 adding 'janis_core/ingestion/galaxy/gxwrappers/__init__.py' 2023-09-27T07:49:07,688 adding 'janis_core/ingestion/galaxy/gxwrappers/downloads/__init__.py' 2023-09-27T07:49:07,690 adding 'janis_core/ingestion/galaxy/gxwrappers/downloads/cache.py' 2023-09-27T07:49:07,691 adding 'janis_core/ingestion/galaxy/gxwrappers/downloads/wrappers.py' 2023-09-27T07:49:07,693 adding 'janis_core/ingestion/galaxy/gxwrappers/requests/__init__.py' 2023-09-27T07:49:07,694 adding 'janis_core/ingestion/galaxy/gxwrappers/requests/versions.py' 2023-09-27T07:49:07,695 adding 'janis_core/ingestion/galaxy/gxwrappers/scraping/__init__.py' 2023-09-27T07:49:07,697 adding 'janis_core/ingestion/galaxy/gxwrappers/scraping/repositories.py' 2023-09-27T07:49:07,698 adding 'janis_core/ingestion/galaxy/gxwrappers/scraping/revisions.py' 2023-09-27T07:49:07,699 adding 'janis_core/ingestion/galaxy/gxwrappers/scraping/scraping.py' 2023-09-27T07:49:07,700 adding 'janis_core/ingestion/galaxy/gxwrappers/scraping/single.py' 2023-09-27T07:49:07,701 adding 'janis_core/ingestion/galaxy/gxwrappers/scraping/utils.py' 2023-09-27T07:49:07,703 adding 'janis_core/ingestion/galaxy/gxwrappers/scraping/wrappers.py' 2023-09-27T07:49:07,705 adding 'janis_core/ingestion/galaxy/gxwrappers/wrappers/Wrapper.py' 2023-09-27T07:49:07,706 adding 'janis_core/ingestion/galaxy/gxwrappers/wrappers/WrapperCache.py' 2023-09-27T07:49:07,708 adding 'janis_core/ingestion/galaxy/gxwrappers/wrappers/__init__.py' 2023-09-27T07:49:07,709 adding 'janis_core/ingestion/galaxy/internal_mapping/__init__.py' 2023-09-27T07:49:07,711 adding 'janis_core/ingestion/galaxy/internal_mapping/main.py' 2023-09-27T07:49:07,713 adding 'janis_core/ingestion/galaxy/internal_model/__init__.py' 2023-09-27T07:49:07,714 adding 'janis_core/ingestion/galaxy/internal_model/protocols.py' 2023-09-27T07:49:07,716 adding 'janis_core/ingestion/galaxy/internal_model/tool/__init__.py' 2023-09-27T07:49:07,718 adding 'janis_core/ingestion/galaxy/internal_model/tool/generate.py' 2023-09-27T07:49:07,720 adding 'janis_core/ingestion/galaxy/internal_model/tool/outputs.py' 2023-09-27T07:49:07,721 adding 'janis_core/ingestion/galaxy/internal_model/tool/tool.py' 2023-09-27T07:49:07,723 adding 'janis_core/ingestion/galaxy/internal_model/workflow/__init__.py' 2023-09-27T07:49:07,725 adding 'janis_core/ingestion/galaxy/internal_model/workflow/input.py' 2023-09-27T07:49:07,726 adding 'janis_core/ingestion/galaxy/internal_model/workflow/metadata.py' 2023-09-27T07:49:07,727 adding 'janis_core/ingestion/galaxy/internal_model/workflow/workflow.py' 2023-09-27T07:49:07,729 adding 'janis_core/ingestion/galaxy/internal_model/workflow/registers/StepInputRegister.py' 2023-09-27T07:49:07,730 adding 'janis_core/ingestion/galaxy/internal_model/workflow/registers/StepOutputRegister.py' 2023-09-27T07:49:07,731 adding 'janis_core/ingestion/galaxy/internal_model/workflow/registers/__init__.py' 2023-09-27T07:49:07,733 adding 'janis_core/ingestion/galaxy/internal_model/workflow/step/__init__.py' 2023-09-27T07:49:07,734 adding 'janis_core/ingestion/galaxy/internal_model/workflow/step/inputs.py' 2023-09-27T07:49:07,735 adding 'janis_core/ingestion/galaxy/internal_model/workflow/step/metadata.py' 2023-09-27T07:49:07,736 adding 'janis_core/ingestion/galaxy/internal_model/workflow/step/outputs.py' 2023-09-27T07:49:07,738 adding 'janis_core/ingestion/galaxy/internal_model/workflow/step/post_step.txt' 2023-09-27T07:49:07,739 adding 'janis_core/ingestion/galaxy/internal_model/workflow/step/step.py' 2023-09-27T07:49:07,740 adding 'janis_core/ingestion/galaxy/janis_mapping/__init__.py' 2023-09-27T07:49:07,742 adding 'janis_core/ingestion/galaxy/janis_mapping/general.py' 2023-09-27T07:49:07,743 adding 'janis_core/ingestion/galaxy/janis_mapping/tool.py' 2023-09-27T07:49:07,745 adding 'janis_core/ingestion/galaxy/janis_mapping/workflow.py' 2023-09-27T07:49:07,746 adding 'janis_core/ingestion/galaxy/messages/__init__.py' 2023-09-27T07:49:07,747 adding 'janis_core/ingestion/galaxy/messages/logs.py' 2023-09-27T07:49:07,748 adding 'janis_core/ingestion/galaxy/messages/messages.py' 2023-09-27T07:49:07,750 adding 'janis_core/ingestion/galaxy/regex_to_glob/__init__.py' 2023-09-27T07:49:07,751 adding 'janis_core/ingestion/galaxy/regex_to_glob/common.py' 2023-09-27T07:49:07,752 adding 'janis_core/ingestion/galaxy/regex_to_glob/convert.py' 2023-09-27T07:49:07,754 adding 'janis_core/ingestion/galaxy/regex_to_glob/patterns.py' 2023-09-27T07:49:07,755 adding 'janis_core/ingestion/galaxy/runtime/__init__.py' 2023-09-27T07:49:07,756 adding 'janis_core/ingestion/galaxy/runtime/dates.py' 2023-09-27T07:49:07,757 adding 'janis_core/ingestion/galaxy/runtime/exceptions.py' 2023-09-27T07:49:07,758 adding 'janis_core/ingestion/galaxy/runtime/general.py' 2023-09-27T07:49:07,759 adding 'janis_core/ingestion/galaxy/runtime/tool.py' 2023-09-27T07:49:07,761 adding 'janis_core/ingestion/galaxy/runtime/startup/__init__.py' 2023-09-27T07:49:07,763 adding 'janis_core/ingestion/galaxy/runtime/startup/tool.py' 2023-09-27T07:49:07,764 adding 'janis_core/ingestion/galaxy/runtime/startup/workflow.py' 2023-09-27T07:49:07,765 adding 'janis_core/ingestion/galaxy/tags/__init__.py' 2023-09-27T07:49:07,767 adding 'janis_core/ingestion/galaxy/tags/groups.py' 2023-09-27T07:49:07,768 adding 'janis_core/ingestion/galaxy/tags/manager.py' 2023-09-27T07:49:07,769 adding 'janis_core/ingestion/galaxy/tags/rules.py' 2023-09-27T07:49:07,771 adding 'janis_core/ingestion/galaxy/tags/strategies.py' 2023-09-27T07:49:07,772 adding 'janis_core/ingestion/galaxy/utils/__init__.py' 2023-09-27T07:49:07,773 adding 'janis_core/ingestion/galaxy/utils/galaxy.py' 2023-09-27T07:49:07,775 adding 'janis_core/ingestion/galaxy/utils/general.py' 2023-09-27T07:49:07,776 adding 'janis_core/ingestion/wdl/__init__.py' 2023-09-27T07:49:07,778 adding 'janis_core/ingestion/wdl/main.py' 2023-09-27T07:49:07,780 adding 'janis_core/messages/__init__.py' 2023-09-27T07:49:07,781 adding 'janis_core/messages/config.yaml' 2023-09-27T07:49:07,783 adding 'janis_core/messages/logfile.py' 2023-09-27T07:49:07,784 adding 'janis_core/messages/main.py' 2023-09-27T07:49:07,786 adding 'janis_core/operators/__init__.py' 2023-09-27T07:49:07,788 adding 'janis_core/operators/logical.py' 2023-09-27T07:49:07,789 adding 'janis_core/operators/operator.py' 2023-09-27T07:49:07,792 adding 'janis_core/operators/selectors.py' 2023-09-27T07:49:07,794 adding 'janis_core/operators/standard.py' 2023-09-27T07:49:07,796 adding 'janis_core/operators/stringformatter.py' 2023-09-27T07:49:07,798 adding 'janis_core/redefinitions/__init__.py' 2023-09-27T07:49:07,801 adding 'janis_core/redefinitions/types.py' 2023-09-27T07:49:07,802 adding 'janis_core/redefinitions/utils.py' 2023-09-27T07:49:07,804 adding 'janis_core/redefinitions/tools/__init__.py' 2023-09-27T07:49:07,806 adding 'janis_core/redefinitions/tools/addbamstats.py' 2023-09-27T07:49:07,808 adding 'janis_core/redefinitions/tools/bcftools.py' 2023-09-27T07:49:07,810 adding 'janis_core/redefinitions/tools/bedtoolsgenomecoverage.py' 2023-09-27T07:49:07,812 adding 'janis_core/redefinitions/tools/bgzip.py' 2023-09-27T07:49:07,813 adding 'janis_core/redefinitions/tools/bioinformaticstool.py' 2023-09-27T07:49:07,815 adding 'janis_core/redefinitions/tools/bwamem_samtoolsview.py' 2023-09-27T07:49:07,817 adding 'janis_core/redefinitions/tools/cat.py' 2023-09-27T07:49:07,818 adding 'janis_core/redefinitions/tools/combinevariants.py' 2023-09-27T07:49:07,821 adding 'janis_core/redefinitions/tools/cutadapt.py' 2023-09-27T07:49:07,822 adding 'janis_core/redefinitions/tools/echo.py' 2023-09-27T07:49:07,824 adding 'janis_core/redefinitions/tools/fastqc.py' 2023-09-27T07:49:07,833 adding 'janis_core/redefinitions/tools/gatk4.py' 2023-09-27T07:49:07,836 adding 'janis_core/redefinitions/tools/generate.py' 2023-09-27T07:49:07,839 adding 'janis_core/redefinitions/tools/gridss.py' 2023-09-27T07:49:07,841 adding 'janis_core/redefinitions/tools/manta.py' 2023-09-27T07:49:07,843 adding 'janis_core/redefinitions/tools/parse.py' 2023-09-27T07:49:07,844 adding 'janis_core/redefinitions/tools/performancesummary.py' 2023-09-27T07:49:07,845 adding 'janis_core/redefinitions/tools/petermacutils.py' 2023-09-27T07:49:07,848 adding 'janis_core/redefinitions/tools/samtools.py' 2023-09-27T07:49:07,850 adding 'janis_core/redefinitions/tools/splitmultiallele.py' 2023-09-27T07:49:07,852 adding 'janis_core/redefinitions/tools/strelka.py' 2023-09-27T07:49:07,854 adding 'janis_core/redefinitions/tools/tabix.py' 2023-09-27T07:49:07,855 adding 'janis_core/redefinitions/tools/trimiupac.py' 2023-09-27T07:49:07,857 adding 'janis_core/redefinitions/tools/uncompressarchive.py' 2023-09-27T07:49:07,859 adding 'janis_core/redefinitions/tools/vardict.py' 2023-09-27T07:49:07,860 adding 'janis_core/redefinitions/tools/vcftools.py' 2023-09-27T07:49:07,862 adding 'janis_core/redefinitions/workflows/__init__.py' 2023-09-27T07:49:07,864 adding 'janis_core/redefinitions/workflows/addbamstats.py' 2023-09-27T07:49:07,865 adding 'janis_core/redefinitions/workflows/bioinformaticsworkflow.py' 2023-09-27T07:49:07,866 adding 'janis_core/redefinitions/workflows/bwaaligner.py' 2023-09-27T07:49:07,868 adding 'janis_core/redefinitions/workflows/gatkbaserecalbqsr.py' 2023-09-27T07:49:07,869 adding 'janis_core/redefinitions/workflows/gatkgermlinevariantcaller.py' 2023-09-27T07:49:07,871 adding 'janis_core/redefinitions/workflows/illuminagermlinevariantcaller.py' 2023-09-27T07:49:07,873 adding 'janis_core/redefinitions/workflows/mergeandmark.py' 2023-09-27T07:49:07,874 adding 'janis_core/redefinitions/workflows/performancesummarygenome.py' 2023-09-27T07:49:07,875 adding 'janis_core/redefinitions/workflows/vardictgermlinevariantcaller.py' 2023-09-27T07:49:07,878 adding 'janis_core/redefinitions/workflows/wgsgermline.py' 2023-09-27T07:49:07,880 adding 'janis_core/settings/__init__.py' 2023-09-27T07:49:07,881 adding 'janis_core/settings/datatypes.py' 2023-09-27T07:49:07,883 adding 'janis_core/settings/graph.py' 2023-09-27T07:49:07,884 adding 'janis_core/settings/testing.py' 2023-09-27T07:49:07,885 adding 'janis_core/settings/validation.py' 2023-09-27T07:49:07,887 adding 'janis_core/settings/ingest/__init__.py' 2023-09-27T07:49:07,888 adding 'janis_core/settings/ingest/cwl.py' 2023-09-27T07:49:07,889 adding 'janis_core/settings/ingest/galaxy.py' 2023-09-27T07:49:07,890 adding 'janis_core/settings/ingest/general.py' 2023-09-27T07:49:07,892 adding 'janis_core/settings/translate/__init__.py' 2023-09-27T07:49:07,893 adding 'janis_core/settings/translate/general.py' 2023-09-27T07:49:07,894 adding 'janis_core/settings/translate/nextflow.py' 2023-09-27T07:49:07,896 adding 'janis_core/tests/__init__.py' 2023-09-27T07:49:07,898 adding 'janis_core/tests/test_commandtool.py' 2023-09-27T07:49:07,899 adding 'janis_core/tests/test_conditionals.py' 2023-09-27T07:49:07,900 adding 'janis_core/tests/test_generics_util.py' 2023-09-27T07:49:07,903 adding 'janis_core/tests/test_ingestion_cwl.py' 2023-09-27T07:49:07,907 adding 'janis_core/tests/test_ingestion_galaxy.py' 2023-09-27T07:49:07,909 adding 'janis_core/tests/test_ingestion_wdl.py' 2023-09-27T07:49:07,913 adding 'janis_core/tests/test_janis_translate.py' 2023-09-27T07:49:07,914 adding 'janis_core/tests/test_logger.py' 2023-09-27T07:49:07,916 adding 'janis_core/tests/test_metadata.py' 2023-09-27T07:49:07,917 adding 'janis_core/tests/test_operators.py' 2023-09-27T07:49:07,918 adding 'janis_core/tests/test_python_tool.py' 2023-09-27T07:49:07,919 adding 'janis_core/tests/test_receivefrom.py' 2023-09-27T07:49:07,920 adding 'janis_core/tests/test_running.py' 2023-09-27T07:49:07,922 adding 'janis_core/tests/test_secondary.py' 2023-09-27T07:49:07,923 adding 'janis_core/tests/test_step.py' 2023-09-27T07:49:07,924 adding 'janis_core/tests/test_stringbuilder.py' 2023-09-27T07:49:07,926 adding 'janis_core/tests/test_test_runner.py' 2023-09-27T07:49:07,927 adding 'janis_core/tests/test_tools.py' 2023-09-27T07:49:07,932 adding 'janis_core/tests/test_translation_cwl.py' 2023-09-27T07:49:07,933 adding 'janis_core/tests/test_translation_modules.py' 2023-09-27T07:49:07,944 adding 'janis_core/tests/test_translation_nextflow.py' 2023-09-27T07:49:07,951 adding 'janis_core/tests/test_translation_wdl.py' 2023-09-27T07:49:07,953 adding 'janis_core/tests/test_types.py' 2023-09-27T07:49:07,955 adding 'janis_core/tests/test_validateinputvalue.py' 2023-09-27T07:49:07,956 adding 'janis_core/tests/test_validators.py' 2023-09-27T07:49:07,958 adding 'janis_core/tests/test_workflow.py' 2023-09-27T07:49:07,959 adding 'janis_core/tests/tests_util.py' 2023-09-27T07:49:09,611 adding 'janis_core/tests/data/aln.sam' 2023-09-27T07:49:09,788 adding 'janis_core/tests/data/aln.sorted.bam' 2023-09-27T07:49:09,800 adding 'janis_core/tests/data/aln.sorted.bam.bai' 2023-09-27T07:49:11,470 adding 'janis_core/tests/data/mutant_R1.fastq' 2023-09-27T07:49:11,505 adding 'janis_core/tests/data/test.txt' 2023-09-27T07:49:11,506 adding 'janis_core/tests/data/test_diff.txt' 2023-09-27T07:49:11,614 adding 'janis_core/tests/data/wildtype.fna' 2023-09-27T07:49:11,619 adding 'janis_core/tests/data/cwl/tools/BasicTestTool.cwl' 2023-09-27T07:49:11,620 adding 'janis_core/tests/data/cwl/tools/bwamem.cwl' 2023-09-27T07:49:11,622 adding 'janis_core/tests/data/cwl/tools/echo.cwl' 2023-09-27T07:49:11,623 adding 'janis_core/tests/data/cwl/tools/fastqc.cwl' 2023-09-27T07:49:11,625 adding 'janis_core/tests/data/cwl/tools/fastqc2.cwl' 2023-09-27T07:49:11,626 adding 'janis_core/tests/data/cwl/tools/gatk_haplotype_caller.cwl' 2023-09-27T07:49:11,631 adding 'janis_core/tests/data/cwl/tools/gatk_haplotype_caller_long.cwl' 2023-09-27T07:49:11,632 adding 'janis_core/tests/data/cwl/tools/rename_png.cwl' 2023-09-27T07:49:11,634 adding 'janis_core/tests/data/cwl/tools/rose.cwl' 2023-09-27T07:49:11,635 adding 'janis_core/tests/data/cwl/tools/samtools_flagstat.cwl' 2023-09-27T07:49:11,637 adding 'janis_core/tests/data/cwl/tools/datatypes/array_types.cwl' 2023-09-27T07:49:11,638 adding 'janis_core/tests/data/cwl/tools/datatypes/basic_types.cwl' 2023-09-27T07:49:11,639 adding 'janis_core/tests/data/cwl/tools/datatypes/secondary_types.cwl' 2023-09-27T07:49:11,641 adding 'janis_core/tests/data/cwl/tools/expressions/inputs_arguments.cwl' 2023-09-27T07:49:11,643 adding 'janis_core/tests/data/cwl/tools/expressions/outputs.cwl' 2023-09-27T07:49:11,644 adding 'janis_core/tests/data/cwl/tools/expressions/requirements.cwl' 2023-09-27T07:49:11,646 adding 'janis_core/tests/data/cwl/tools/expressions/resources.cwl' 2023-09-27T07:49:11,647 adding 'janis_core/tests/data/cwl/tools/expressions/streams.cwl' 2023-09-27T07:49:11,649 adding 'janis_core/tests/data/cwl/tools/expressiontools/check_value.cwl' 2023-09-27T07:49:11,651 adding 'janis_core/tests/data/cwl/tools/requirements/add_crossmapped2resmapped.cwl' 2023-09-27T07:49:11,653 adding 'janis_core/tests/data/cwl/tools/requirements/amplicon_architect.cwl' 2023-09-27T07:49:11,654 adding 'janis_core/tests/data/cwl/tools/requirements/antismash_v4.cwl' 2023-09-27T07:49:11,656 adding 'janis_core/tests/data/cwl/tools/requirements/bundle_secondaryfiles.cwl' 2023-09-27T07:49:11,657 adding 'janis_core/tests/data/cwl/tools/requirements/check_threshold.cwl' 2023-09-27T07:49:11,662 adding 'janis_core/tests/data/cwl/tools/requirements/control-freec-11-6-sbg.cwl' 2023-09-27T07:49:11,663 adding 'janis_core/tests/data/cwl/tools/requirements/prepare_fasta_db.cwl' 2023-09-27T07:49:11,665 adding 'janis_core/tests/data/cwl/tools/requirements/return_directory.cwl' 2023-09-27T07:49:11,667 adding 'janis_core/tests/data/cwl/tools/requirements/Python/add_crossmapped2resmapped.py' 2023-09-27T07:49:11,668 adding 'janis_core/tests/data/cwl/tools/requirements/Python/check_threshold.py' 2023-09-27T07:49:11,670 adding 'janis_core/tests/data/cwl/workflows/expressions.cwl' 2023-09-27T07:49:11,672 adding 'janis_core/tests/data/cwl/workflows/super_enhancer_wf.cwl' 2023-09-27T07:49:11,674 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/CONTRIBUTING.md' 2023-09-27T07:49:11,676 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/CroMaSt.cwl' 2023-09-27T07:49:11,678 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/LICENSE' 2023-09-27T07:49:11,679 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/README.md' 2023-09-27T07:49:11,682 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/ro-crate-metadata.json' 2023-09-27T07:49:11,686 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/ro-crate-preview.html' 2023-09-27T07:49:11,697 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/workflow-390-9f3832867eab6c7a6363f8ca594a4bcf2ff7e96f-diagram.svg' 2023-09-27T07:49:11,700 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/add_crossmapped2resmapped.cwl' 2023-09-27T07:49:11,701 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/add_domain_num.cwl' 2023-09-27T07:49:11,703 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/align_compute_avg.cwl' 2023-09-27T07:49:11,704 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/check_threshold.cwl' 2023-09-27T07:49:11,706 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/chop_struct2domains.cwl' 2023-09-27T07:49:11,707 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/compare_cath_pfam.cwl' 2023-09-27T07:49:11,709 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/core_avg_subwf.cwl' 2023-09-27T07:49:11,710 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/create_param.cwl' 2023-09-27T07:49:11,711 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/crossmapped_per_unp_dom.cwl' 2023-09-27T07:49:11,713 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/download_data.cwl' 2023-09-27T07:49:11,714 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/filter_align_scores.cwl' 2023-09-27T07:49:11,716 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/gather_lost_resmap.cwl' 2023-09-27T07:49:11,717 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/get_family_ids.cwl' 2023-09-27T07:49:11,719 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/list_true_domains.cwl' 2023-09-27T07:49:11,720 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/map_unique_struct_cath2pfam.cwl' 2023-09-27T07:49:11,722 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/map_unique_struct_pfam2cath.cwl' 2023-09-27T07:49:11,724 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/merge_df2json.cwl' 2023-09-27T07:49:11,725 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/move_files.cwl' 2023-09-27T07:49:11,727 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/other_avg_subwf.cwl' 2023-09-27T07:49:11,728 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/pairwise_aligner.cwl' 2023-09-27T07:49:11,730 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/resmapping_cath2up.cwl' 2023-09-27T07:49:11,731 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/resmapping_cath_instances_subwf.cwl' 2023-09-27T07:49:11,733 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/resmapping_pfam2pdb.cwl' 2023-09-27T07:49:11,734 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/resmapping_pfam_instances_subwf.cwl' 2023-09-27T07:49:11,736 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/separate_cath.cwl' 2023-09-27T07:49:11,738 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/separate_pfam.cwl' 2023-09-27T07:49:11,739 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/unmapped_unp_avg_align.cwl' 2023-09-27T07:49:11,741 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/add_crossmapped2resmapped.py' 2023-09-27T07:49:11,743 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/add_domain_num.py' 2023-09-27T07:49:11,745 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/align_compute_avg.py' 2023-09-27T07:49:11,746 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/check_threshold.py' 2023-09-27T07:49:11,748 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/chop_struct2domains.py' 2023-09-27T07:49:11,749 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/compare_cath_pfam.py' 2023-09-27T07:49:11,751 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/create_param.py' 2023-09-27T07:49:11,752 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/crossmapped_per_unp_dom.py' 2023-09-27T07:49:11,753 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/filter_align_scores.py' 2023-09-27T07:49:11,755 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/get_family_ids.py' 2023-09-27T07:49:11,756 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/map_unique_struct_cath2pfam.py' 2023-09-27T07:49:11,757 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/map_unique_struct_pfam2cath.py' 2023-09-27T07:49:11,759 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/merge_df2json.py' 2023-09-27T07:49:11,760 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/pairwise_aligner.py' 2023-09-27T07:49:11,762 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/residue_mapping.py' 2023-09-27T07:49:11,763 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/resmapping_cath2up.py' 2023-09-27T07:49:11,765 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/resmapping_pfam2pdb.py' 2023-09-27T07:49:11,766 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/separate_cath.py' 2023-09-27T07:49:11,767 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/Tools/Python/separate_pfam.py' 2023-09-27T07:49:11,769 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/translated/main.nf' 2023-09-27T07:49:11,771 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/yml/CroMaSt_input.yml' 2023-09-27T07:49:11,773 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/yml/download_data.yml' 2023-09-27T07:49:11,774 adding 'janis_core/tests/data/cwl/workflows/CroMaSt/yml/environment.yml' 2023-09-27T07:49:11,776 adding 'janis_core/tests/data/cwl/workflows/align_sort_markdup/align_sort_markdup.cwl' 2023-09-27T07:49:11,778 adding 'janis_core/tests/data/cwl/workflows/align_sort_markdup/subworkflows/align.cwl' 2023-09-27T07:49:11,780 adding 'janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/align_and_tag.cwl' 2023-09-27T07:49:11,781 adding 'janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/index_bam.cwl' 2023-09-27T07:49:11,782 adding 'janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/mark_duplicates_and_sort.cwl' 2023-09-27T07:49:11,783 adding 'janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/merge_bams_samtools.cwl' 2023-09-27T07:49:11,785 adding 'janis_core/tests/data/cwl/workflows/align_sort_markdup/tools/name_sort.cwl' 2023-09-27T07:49:11,787 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/pipelines/alignment_exome.cwl' 2023-09-27T07:49:11,789 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/align.cwl' 2023-09-27T07:49:11,790 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/align_sort_markdup.cwl' 2023-09-27T07:49:11,792 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/hs_metrics.cwl' 2023-09-27T07:49:11,793 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/qc_exome.cwl' 2023-09-27T07:49:11,795 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/sequence_align_and_tag_adapter.cwl' 2023-09-27T07:49:11,796 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/subworkflows/sequence_to_bqsr.cwl' 2023-09-27T07:49:11,798 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/align_and_tag.cwl' 2023-09-27T07:49:11,799 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/apply_bqsr.cwl' 2023-09-27T07:49:11,800 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/bqsr.cwl' 2023-09-27T07:49:11,802 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/collect_alignment_summary_metrics.cwl' 2023-09-27T07:49:11,803 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/collect_hs_metrics.cwl' 2023-09-27T07:49:11,804 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/collect_insert_size_metrics.cwl' 2023-09-27T07:49:11,806 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/gatk_haplotype_caller.cwl' 2023-09-27T07:49:11,807 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/index_bam.cwl' 2023-09-27T07:49:11,808 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/mark_duplicates_and_sort.cwl' 2023-09-27T07:49:11,810 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/merge_bams.cwl' 2023-09-27T07:49:11,811 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/merge_bams_samtools.cwl' 2023-09-27T07:49:11,812 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/name_sort.cwl' 2023-09-27T07:49:11,813 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/samtools_flagstat.cwl' 2023-09-27T07:49:11,814 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/select_variants.cwl' 2023-09-27T07:49:11,816 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/sequence_align_and_tag.cwl' 2023-09-27T07:49:11,817 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/tools/verify_bam_id.cwl' 2023-09-27T07:49:11,819 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/types/labelled_file.yml' 2023-09-27T07:49:11,820 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/types/sequence_data.yml' 2023-09-27T07:49:11,821 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/types/trimming_options.yml' 2023-09-27T07:49:11,822 adding 'janis_core/tests/data/cwl/workflows/analysis-workflows/types/vep_custom_annotation.yml' 2023-09-27T07:49:11,825 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-output_formats.yaml' 2023-09-27T07:49:11,827 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-strand_values.yaml' 2023-09-27T07:49:11,828 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastp-v0.9.21.cwl' 2023-09-27T07:49:11,829 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastp-v0.9.21.test.job.yaml' 2023-09-27T07:49:11,831 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastp-v0.9.21_docker.cwl' 2023-09-27T07:49:11,833 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastx-v0.9.21.cwl' 2023-09-27T07:49:11,834 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.blastx-v0.9.21.test.job.yaml' 2023-09-27T07:49:11,836 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.makedb-v0.9.21.cwl' 2023-09-27T07:49:11,837 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond.makedb-v0.9.21.test.job.yaml' 2023-09-27T07:49:11,838 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond_blastp_test.yml' 2023-09-27T07:49:11,840 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond_blastx_test.yml' 2023-09-27T07:49:11,841 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/diamond-subwf.cwl' 2023-09-27T07:49:11,842 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/diamond-subwf.yml' 2023-09-27T07:49:11,844 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Dockerfile' 2023-09-27T07:49:11,845 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_join.cwl' 2023-09-27T07:49:11,846 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_join.job.yaml' 2023-09-27T07:49:11,847 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_join.test.yaml' 2023-09-27T07:49:11,848 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/diamond_post_run_join.sh' 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'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/example_diamond_10' 2023-09-27T07:49:11,859 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/example_diamond_10_sorted' 2023-09-27T07:49:11,860 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/example_diamond_db' 2023-09-27T07:49:11,862 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Diamond/Diamond-Post-Processing/Files/output_example/example_diamond_10_sorted_join' 2023-09-27T07:49:11,864 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggnog-subwf.cwl' 2023-09-27T07:49:11,865 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggnog-subwf.yml' 2023-09-27T07:49:11,867 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/Dockerfile' 2023-09-27T07:49:11,868 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnog.cwl' 2023-09-27T07:49:11,870 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnog.yml' 2023-09-27T07:49:11,875 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/emapper.py' 2023-09-27T07:49:11,877 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/__init__.py' 2023-09-27T07:49:11,879 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/annota.py' 2023-09-27T07:49:11,881 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/EggNOG/eggNOG/eggnogmapper/annota_mongo.py' 2023-09-27T07:49:11,883 adding 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'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/KEGG_pathways/kegg_pathways.yml' 2023-09-27T07:49:12,132 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Modification/modification_table.cwl' 2023-09-27T07:49:12,134 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Modification/modification_table.yml' 2023-09-27T07:49:12,135 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan/parsing_hmmscan.cwl' 2023-09-27T07:49:12,137 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan/parsing_hmmscan.py' 2023-09-27T07:49:12,138 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/Parsing_hmmscan/parsing_hmmscan.yml' 2023-09-27T07:49:12,140 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/expected-output/assembly-SRR1620013_small_FASTA_FASTA.summary.kegg_contigs.tsv' 2023-09-27T07:49:12,141 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/KEGG_analysis/expected-output/assembly-SRR1620013_small_FASTA_FASTA.summary.kegg_pathways' 2023-09-27T07:49:12,143 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/Viral/Dockerfile' 2023-09-27T07:49:12,145 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash_chunking_subwf.cwl' 2023-09-27T07:49:12,147 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash_subwf.cwl' 2023-09-27T07:49:12,148 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/filtering_fasta_for_antismash.cwl' 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'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_geneclusters_txt/change_geneclusters_ctg.py' 2023-09-27T07:49:12,165 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/fix_geneclusters_txt/change_geneclusters_txt.cwl' 2023-09-27T07:49:12,167 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash/antismash_to_gff.cwl' 2023-09-27T07:49:12,169 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash/antismash_to_gff.py' 2023-09-27T07:49:12,170 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/post-processing/gff_antismash/antismash_to_gff.yml' 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'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/avg_chopped_structures_unp_domains.nf' 2023-09-27T07:49:13,533 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bam_index.nf' 2023-09-27T07:49:13,534 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bed_to_bigbed.nf' 2023-09-27T07:49:13,535 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bed_to_macs.nf' 2023-09-27T07:49:13,536 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bundle_secondaries.nf' 2023-09-27T07:49:13,538 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/bwa_index.nf' 2023-09-27T07:49:13,539 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/carveme.nf' 2023-09-27T07:49:13,540 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/carveme_files_to_folder.nf' 2023-09-27T07:49:13,541 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/cat.nf' 2023-09-27T07:49:13,542 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/cat_models.nf' 2023-09-27T07:49:13,544 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/check_alignment_scores.nf' 2023-09-27T07:49:13,545 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/check_threshold_step.nf' 2023-09-27T07:49:13,546 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chinking_SC_fasta_nucleotide.nf' 2023-09-27T07:49:13,547 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chinking_fasta_nucleotide.nf' 2023-09-27T07:49:13,548 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chinking_fasta_proteins.nf' 2023-09-27T07:49:13,550 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chop_structs.nf' 2023-09-27T07:49:13,551 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/chunking_tsv.nf' 2023-09-27T07:49:13,552 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/classifications_to_otu_counts.nf' 2023-09-27T07:49:13,553 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/clean_classification.nf' 2023-09-27T07:49:13,554 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/clean_fasta_headers.nf' 2023-09-27T07:49:13,555 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/cmsearch.nf' 2023-09-27T07:49:13,557 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/collect_lost_instances.nf' 2023-09-27T07:49:13,558 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/combine.nf' 2023-09-27T07:49:13,559 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/combine_ips.nf' 2023-09-27T07:49:13,560 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/combine_trimmed.nf' 2023-09-27T07:49:13,562 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compare_instances_CATH_Pfam.nf' 2023-09-27T07:49:13,563 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compress.nf' 2023-09-27T07:49:13,564 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compress_carveme.nf' 2023-09-27T07:49:13,565 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compress_mapseq.nf' 2023-09-27T07:49:13,566 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compress_prodigal.nf' 2023-09-27T07:49:13,567 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/compression.nf' 2023-09-27T07:49:13,569 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/conversion.nf' 2023-09-27T07:49:13,570 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/convert_trimmed_reads_to_fasta.nf' 2023-09-27T07:49:13,571 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/copy_avg_dom.nf' 2023-09-27T07:49:13,572 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_ITS_seqs.nf' 2023-09-27T07:49:13,574 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_cds.nf' 2023-09-27T07:49:13,575 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_lines_mapseq.nf' 2023-09-27T07:49:13,576 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_lsu_fasta.nf' 2023-09-27T07:49:13,577 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_masked_fasta.nf' 2023-09-27T07:49:13,578 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_overlapped_reads.nf' 2023-09-27T07:49:13,579 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_processed_reads.nf' 2023-09-27T07:49:13,581 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_ssu_fasta.nf' 2023-09-27T07:49:13,582 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_submitted_reads.nf' 2023-09-27T07:49:13,583 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/count_submitted_reads_single.nf' 2023-09-27T07:49:13,584 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/counts_to_hdf5.nf' 2023-09-27T07:49:13,585 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/counts_to_json.nf' 2023-09-27T07:49:13,586 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/create_new_parameters.nf' 2023-09-27T07:49:13,588 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/crossmapping_CATH2Pfam.nf' 2023-09-27T07:49:13,589 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/crossmapping_Pfam2CATH.nf' 2023-09-27T07:49:13,590 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/expressiontool_bam_index.nf' 2023-09-27T07:49:13,591 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/extract_coords.nf' 2023-09-27T07:49:13,592 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/extract_sequences.nf' 2023-09-27T07:49:13,594 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/extract_subunits.nf' 2023-09-27T07:49:13,595 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/extract_subunits_coords.nf' 2023-09-27T07:49:13,596 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/fastqc.nf' 2023-09-27T07:49:13,597 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/fastqc_files_to_folder.nf' 2023-09-27T07:49:13,598 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/filter_cath_structures.nf' 2023-09-27T07:49:13,600 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/filter_paired.nf' 2023-09-27T07:49:13,601 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/filter_pfam_structures.nf' 2023-09-27T07:49:13,602 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/folder_compression.nf' 2023-09-27T07:49:13,603 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/format_core_list.nf' 2023-09-27T07:49:13,605 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/functional_stats.nf' 2023-09-27T07:49:13,606 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gather_domain_like.nf' 2023-09-27T07:49:13,607 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gather_failed_domains.nf' 2023-09-27T07:49:13,608 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gatk_selectvariants_manta.nf' 2023-09-27T07:49:13,609 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gemstats.nf' 2023-09-27T07:49:13,610 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/get_coords.nf' 2023-09-27T07:49:13,612 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/get_family_ids.nf' 2023-09-27T07:49:13,613 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/get_ncrnas.nf' 2023-09-27T07:49:13,614 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/go_summary.nf' 2023-09-27T07:49:13,615 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip.nf' 2023-09-27T07:49:13,616 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip_LSU.nf' 2023-09-27T07:49:13,617 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip_SSU.nf' 2023-09-27T07:49:13,619 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip_files.nf' 2023-09-27T07:49:13,620 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/gzip_masked_ITS.nf' 2023-09-27T07:49:13,621 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/hashsum_paired.nf' 2023-09-27T07:49:13,622 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/hashsum_single.nf' 2023-09-27T07:49:13,623 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/header_addition.nf' 2023-09-27T07:49:13,625 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/hmmsearch.nf' 2023-09-27T07:49:13,626 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/index_reads.nf' 2023-09-27T07:49:13,627 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/index_strelka_bed.nf' 2023-09-27T07:49:13,628 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/interproscan.nf' 2023-09-27T07:49:13,629 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/kofamscan.nf' 2023-09-27T07:49:13,631 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/length_filter.nf' 2023-09-27T07:49:13,632 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/make_gff.nf' 2023-09-27T07:49:13,633 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/make_tab_sep.nf' 2023-09-27T07:49:13,634 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/manta.nf' 2023-09-27T07:49:13,635 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/mapseq.nf' 2023-09-27T07:49:13,637 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/mask_for_ITS.nf' 2023-09-27T07:49:13,638 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/memote_files_to_folder.nf' 2023-09-27T07:49:13,639 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/memote_report_snapshot.nf' 2023-09-27T07:49:13,640 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/memote_run.nf' 2023-09-27T07:49:13,641 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/motus_classification.nf' 2023-09-27T07:49:13,642 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/move_to_functional_annotation_folder.nf' 2023-09-27T07:49:13,644 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/move_to_seq_cat_folder.nf' 2023-09-27T07:49:13,645 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/ngtax.nf' 2023-09-27T07:49:13,646 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/ngtax_files_to_folder.nf' 2023-09-27T07:49:13,647 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/ngtax_to_tsv_fasta.nf' 2023-09-27T07:49:13,649 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/no_tax_file_flag.nf' 2023-09-27T07:49:13,650 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/overlap_reads.nf' 2023-09-27T07:49:13,651 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/pairwise_align_avg_structs.nf' 2023-09-27T07:49:13,652 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/per_dom_instance.nf' 2023-09-27T07:49:13,653 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/per_unp_dom_instance.nf' 2023-09-27T07:49:13,655 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/pfam.nf' 2023-09-27T07:49:13,656 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Assembly/antismash/chunking_antismash_with_conditionals/translated/modules/phyloseq_files_to_folder.nf' 2023-09-27T07:49:13,657 adding 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adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.fgs.ffn' 2023-09-27T07:49:33,061 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.prodigal' 2023-09-27T07:49:33,119 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.prodigal.faa' 2023-09-27T07:49:33,564 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.prodigal.ffn' 2023-09-27T07:49:33,685 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/ERR3414571_FASTA.cmsearch.all.tblout.deoverlapped' 2023-09-27T07:49:33,695 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/Dockerfile' 2023-09-27T07:49:35,942 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/go-basic-metagenomics_release_20160705.obo' 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'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/hmmscan_tab_modification/test-input/hmmscan_result.tbl' 2023-09-27T07:49:53,491 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv/make_csv.cwl' 2023-09-27T07:49:53,493 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv/make_csv.py' 2023-09-27T07:49:53,494 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv/output' 2023-09-27T07:49:53,495 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/make_csv/test.txt' 2023-09-27T07:49:53,496 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/pigz/gzip.cwl' 2023-09-27T07:49:53,498 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/__init__.py' 2023-09-27T07:49:53,499 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/chunkFastaResultFileUtil.py' 2023-09-27T07:49:53,501 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/chunkTSVFileUtil.py' 2023-09-27T07:49:53,502 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/cleaningUtils.py' 2023-09-27T07:49:53,503 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/result_chunker.cwl' 2023-09-27T07:49:53,505 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/result-file-chunker/run_result_file_chunker.py' 2023-09-27T07:49:53,507 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/test-inputs/test_seqs.fasta' 2023-09-27T07:49:53,508 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/utils/test-inputs/test_seqs.fq' 2023-09-27T07:49:53,510 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/amplicon-wf--v.5-cond.cwl' 2023-09-27T07:49:53,512 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/assembly-wf--v.5-cond.cwl' 2023-09-27T07:49:53,513 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/raw-reads-wf--v.5-cond.cwl' 2023-09-27T07:49:53,515 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/README' 2023-09-27T07:49:53,516 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/out_json_parser.py' 2023-09-27T07:49:53,518 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/amplicon/amplicon-1.cwl' 2023-09-27T07:49:53,520 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/amplicon/amplicon-2.cwl' 2023-09-27T07:49:53,522 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/assembly/assembly-1.cwl' 2023-09-27T07:49:53,523 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/assembly/assembly-2.cwl' 2023-09-27T07:49:53,526 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/raw-reads/raw-reads-1.cwl' 2023-09-27T07:49:53,527 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/conditionals/raw-reads/raw-reads-2.cwl' 2023-09-27T07:49:53,529 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/profiling/profiling_parser.py' 2023-09-27T07:49:53,530 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/profiling/run_profiling.sh' 2023-09-27T07:49:53,532 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/chunking-subwf-IPS.cwl' 2023-09-27T07:49:53,534 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/chunking-subwf-hmmsearch.cwl' 2023-09-27T07:49:53,535 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/classify-otu-visualise.cwl' 2023-09-27T07:49:53,536 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/cmsearch-condition.cwl' 2023-09-27T07:49:53,537 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/cmsearch-multimodel-raw-data.cwl' 2023-09-27T07:49:53,539 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/final_chunking.cwl' 2023-09-27T07:49:53,540 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/func_summaries.cwl' 2023-09-27T07:49:53,542 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/other_ncrnas.cwl' 2023-09-27T07:49:53,543 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/rna_prediction-sub-wf.cwl' 2023-09-27T07:49:53,545 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/seqprep-subwf.cwl' 2023-09-27T07:49:53,547 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon/ITS-wf.cwl' 2023-09-27T07:49:53,548 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon/trim_and_reformat_reads.cwl' 2023-09-27T07:49:53,549 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/amplicon/trimming-not-empty-subwf.cwl' 2023-09-27T07:49:53,551 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/CGC-subwf.cwl' 2023-09-27T07:49:53,552 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/change_formats_and_names.cwl' 2023-09-27T07:49:53,553 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/cmsearch-multimodel-assembly.cwl' 2023-09-27T07:49:53,554 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/deal_with_functional_annotation.cwl' 2023-09-27T07:49:53,556 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/func_ann_and_post_processing-subwf.cwl' 2023-09-27T07:49:53,557 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/functional_annotation.cwl' 2023-09-27T07:49:53,558 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/functional_annotation.yml' 2023-09-27T07:49:53,560 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/kegg_analysis.cwl' 2023-09-27T07:49:53,561 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/assembly/kegg_analysis.yml' 2023-09-27T07:49:53,563 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads/CGC-subwf.cwl' 2023-09-27T07:49:53,564 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads/func_ann_and_post_proccessing-subwf.cwl' 2023-09-27T07:49:53,565 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads/functional_annotation_raw.cwl' 2023-09-27T07:49:53,567 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/subworkflows/raw_reads/mOTUs-workflow.cwl' 2023-09-27T07:49:53,568 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls/amplicon-wf--v.5-cond.yml' 2023-09-27T07:49:53,570 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls/assembly-pipeline-v.5.yml' 2023-09-27T07:49:53,571 adding 'janis_core/tests/data/cwl/workflows/ebi-metagenomics/workflows/ymls/raw-reads--v.5-cond.yml' 2023-09-27T07:49:53,576 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/README.md' 2023-09-27T07:49:53,581 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/kfdrc_production_somatic_variant_cnv_wf.cwl' 2023-09-27T07:49:53,582 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/samtools_cram2bam_plus_calmd.cwl' 2023-09-27T07:49:53,584 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config/control_freec.cwl' 2023-09-27T07:49:53,586 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config/control_freec_R.cwl' 2023-09-27T07:49:53,587 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config/control_freec_visualize.cwl' 2023-09-27T07:49:53,588 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec11.5_built-in_config/gen_controlfreec_configfile.cwl' 2023-09-27T07:49:53,590 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7/control_freec.cwl' 2023-09-27T07:49:53,591 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7/control_freec_R.cwl' 2023-09-27T07:49:53,592 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/depcrecated/controlFreec8.7/control_freec_visualize.cwl' 2023-09-27T07:49:53,594 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/build_strelka2_mnp.py' 2023-09-27T07:49:53,596 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/cnv_using_subwf_test.cwl' 2023-09-27T07:49:53,597 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/custom_split.py' 2023-09-27T07:49:53,598 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/delme_pbta_temp_vcftomaf.cwl' 2023-09-27T07:49:53,600 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/delme_tcga_temp_vcftomaf.cwl' 2023-09-27T07:49:53,601 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/gatk_intervallisttool.cwl' 2023-09-27T07:49:53,602 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/gatk_sortvcf.cwl' 2023-09-27T07:49:53,603 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/gen_germline_controlfreec_config.cwl' 2023-09-27T07:49:53,605 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/lancet.cwl' 2023-09-27T07:49:53,606 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/output_vcf_pick.py' 2023-09-27T07:49:53,607 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/quick_split_bed.cwl' 2023-09-27T07:49:53,608 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/samtools_index.cwl' 2023-09-27T07:49:53,609 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/temp_rerun_vcf2maf.cwl' 2023-09-27T07:49:53,611 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/dev/vardictjava.cwl' 2023-09-27T07:49:53,613 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/add_strelka2_fields.py' 2023-09-27T07:49:53,616 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/consensus_merge.py' 2023-09-27T07:49:53,619 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/hotspot.py' 2023-09-27T07:49:53,628 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/kf_mskcc_vcf2maf_1.6.21.pl' 2023-09-27T07:49:53,635 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/sbg_cveto_util.py' 2023-09-27T07:49:53,637 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/sbg_multicnv.py' 2023-09-27T07:49:53,639 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/sbg_multicnv_methods.py' 2023-09-27T07:49:53,641 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/scripts/sbg_multicnv_visualisations.py' 2023-09-27T07:49:53,643 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_cnvkit_sub_wf.cwl' 2023-09-27T07:49:53,644 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_controlfreec_sub_wf.cwl' 2023-09-27T07:49:53,648 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_gatk_cnv_somatic_pair_wf.cwl' 2023-09-27T07:49:53,650 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_lancet_sub_wf.cwl' 2023-09-27T07:49:53,651 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_manta_sub_wf.cwl' 2023-09-27T07:49:53,653 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_mutect2_filter_support_subwf.cwl' 2023-09-27T07:49:53,654 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_mutect2_sub_wf.cwl' 2023-09-27T07:49:53,656 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_run_theta2_sub_wf.cwl' 2023-09-27T07:49:53,658 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_strelka2_sub_wf.cwl' 2023-09-27T07:49:53,659 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/kfdrc_vardict_sub_wf.cwl' 2023-09-27T07:49:53,661 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/sub_workflows/prepare_reference.cwl' 2023-09-27T07:49:53,664 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/aa_classifier.cwl' 2023-09-27T07:49:53,665 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/add_basename.cwl' 2023-09-27T07:49:53,667 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/add_strelka2_fields.cwl' 2023-09-27T07:49:53,668 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/amplicon_architect.cwl' 2023-09-27T07:49:53,669 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/annotsv.cwl' 2023-09-27T07:49:53,671 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/awk_min_seg_length.cwl' 2023-09-27T07:49:53,672 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcbio_filter_vardict_somatic.cwl' 2023-09-27T07:49:53,673 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcbio_normalize_vcf.cwl' 2023-09-27T07:49:53,674 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcbio_variant_recall_ensemble.cwl' 2023-09-27T07:49:53,675 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcftools_annotate.cwl' 2023-09-27T07:49:53,677 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcftools_filter_vcf.cwl' 2023-09-27T07:49:53,678 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcftools_reheader_vcf.cwl' 2023-09-27T07:49:53,679 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bcftools_strip_ann.cwl' 2023-09-27T07:49:53,680 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bedtools_intersect.cwl' 2023-09-27T07:49:53,681 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bundle_secondaryfiles.cwl' 2023-09-27T07:49:53,683 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/bwa_index.cwl' 2023-09-27T07:49:53,684 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/canvas_paired_wes.cwl' 2023-09-27T07:49:53,685 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cns_to_aa_bed.cwl' 2023-09-27T07:49:53,687 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_batch.cwl' 2023-09-27T07:49:53,688 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_batch_only.cwl' 2023-09-27T07:49:53,689 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_call.cwl' 2023-09-27T07:49:53,691 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_export_theta2.cwl' 2023-09-27T07:49:53,692 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvkit_import_theta2.cwl' 2023-09-27T07:49:53,694 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/cnvnator.cwl' 2023-09-27T07:49:53,695 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/consensus_merge.cwl' 2023-09-27T07:49:53,700 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/control-freec-11-6-sbg.cwl' 2023-09-27T07:49:53,701 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/control_freec_mini_pileup.cwl' 2023-09-27T07:49:53,702 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/expression_flatten_file_list.cwl' 2023-09-27T07:49:53,704 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/expression_flatten_list.cwl' 2023-09-27T07:49:53,705 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/expression_pickvalue_workaround.cwl' 2023-09-27T07:49:53,706 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/expression_run_aa_if_wgs.cwl' 2023-09-27T07:49:53,708 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_Mutect2.cwl' 2023-09-27T07:49:53,709 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_annotateintervals.cwl' 2023-09-27T07:49:53,711 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_calculatecontamination.cwl' 2023-09-27T07:49:53,712 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_callcopyratiosegments.cwl' 2023-09-27T07:49:53,714 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_collectalleliccounts.cwl' 2023-09-27T07:49:53,715 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_collectreadcounts.cwl' 2023-09-27T07:49:53,716 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_createreadcountpanelofnormals.cwl' 2023-09-27T07:49:53,718 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_denoisereadcounts.cwl' 2023-09-27T07:49:53,719 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_filter_germline_variant.cwl' 2023-09-27T07:49:53,720 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_filtermutectcalls.cwl' 2023-09-27T07:49:53,722 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_funcotatesegments.cwl' 2023-09-27T07:49:53,723 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_gatherpileupsummaries.cwl' 2023-09-27T07:49:53,725 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_getpileupsummaries.cwl' 2023-09-27T07:49:53,726 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_indexfeaturefile.cwl' 2023-09-27T07:49:53,727 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_intervallisttool.cwl' 2023-09-27T07:49:53,729 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_learnorientationbias.cwl' 2023-09-27T07:49:53,730 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_mergemutectstats.cwl' 2023-09-27T07:49:53,731 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_mergevcfs.cwl' 2023-09-27T07:49:53,733 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_modelsegments.cwl' 2023-09-27T07:49:53,734 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_plotdenoisedcopyratios.cwl' 2023-09-27T07:49:53,735 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_plotmodeledsegments.cwl' 2023-09-27T07:49:53,737 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_preprocessintervals.cwl' 2023-09-27T07:49:53,738 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_selectvariants.cwl' 2023-09-27T07:49:53,739 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_sortvcf.cwl' 2023-09-27T07:49:53,741 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/gatk_variant_filter.cwl' 2023-09-27T07:49:53,742 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/generic_rename_outputs.cwl' 2023-09-27T07:49:53,744 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/hotspots_annotation.cwl' 2023-09-27T07:49:53,745 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/kf_mskcc_vcf2maf.cwl' 2023-09-27T07:49:53,746 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/lancet.cwl' 2023-09-27T07:49:53,748 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/lumpy-sv_germline.cwl' 2023-09-27T07:49:53,749 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/lumpy-sv_somatic.cwl' 2023-09-27T07:49:53,750 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/manta.cwl' 2023-09-27T07:49:53,752 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/mode_defaults.cwl' 2023-09-27T07:49:53,753 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/mode_list_selector.cwl' 2023-09-27T07:49:53,754 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/mode_selector.cwl' 2023-09-27T07:49:53,755 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/normalize_vcf.cwl' 2023-09-27T07:49:53,757 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/picard_createsequencedictionary.cwl' 2023-09-27T07:49:53,758 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/prep_mnp_variants.cwl' 2023-09-27T07:49:53,759 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/prepare_aa.cwl' 2023-09-27T07:49:53,761 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/preprocess_lancet_intervals.cwl' 2023-09-27T07:49:53,762 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/python_vardict_interval_split.cwl' 2023-09-27T07:49:53,763 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/samtools_calmd.cwl' 2023-09-27T07:49:53,765 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/samtools_cram2bam.cwl' 2023-09-27T07:49:53,766 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/samtools_faidx.cwl' 2023-09-27T07:49:53,767 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/samtools_reheader_bam.cwl' 2023-09-27T07:49:53,769 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/sb_multicnv_1_0_0.cwl' 2023-09-27T07:49:53,770 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/sb_multicnv_prepare_files_for_scatter.cwl' 2023-09-27T07:49:53,772 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/sb_multicnv_rename_files.cwl' 2023-09-27T07:49:53,773 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/seurat.cwl' 2023-09-27T07:49:53,775 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/smoove_lumpy.cwl' 2023-09-27T07:49:53,776 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/snpEff_annotate.cwl' 2023-09-27T07:49:53,777 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/speedseq_sv_annotate.cwl' 2023-09-27T07:49:53,778 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/strelka2.cwl' 2023-09-27T07:49:53,780 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/tabix_index.cwl' 2023-09-27T07:49:53,781 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/tar.cwl' 2023-09-27T07:49:53,782 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/theta2_purity.cwl' 2023-09-27T07:49:53,784 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/ubuntu_ratio2seg.cwl' 2023-09-27T07:49:53,785 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/ubuntu_rename_outputs.cwl' 2023-09-27T07:49:53,786 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/untar_gzip.cwl' 2023-09-27T07:49:53,788 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/vardictjava.cwl' 2023-09-27T07:49:53,789 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/tools/variant_effect_predictor_105.cwl' 2023-09-27T07:49:53,798 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc-somatic-variant-workflow.cwl' 2023-09-27T07:49:53,801 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_annot_vcf_wf.cwl' 2023-09-27T07:49:53,803 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_consensus_calling.cwl' 2023-09-27T07:49:53,805 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_gatk_create_cnv_pon_wf.cwl' 2023-09-27T07:49:53,807 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_amplicon_architect.cwl' 2023-09-27T07:49:53,809 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_cnvkit_theta2_wf.cwl' 2023-09-27T07:49:53,811 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_cnvkit_wf.cwl' 2023-09-27T07:49:53,812 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_controlfreec_wf.cwl' 2023-09-27T07:49:53,814 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_lancet_wf.cwl' 2023-09-27T07:49:53,816 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_manta_wf.cwl' 2023-09-27T07:49:53,818 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_mutect2_wf.cwl' 2023-09-27T07:49:53,820 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_strelka2_wf.cwl' 2023-09-27T07:49:53,821 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_theta2_wf.cwl' 2023-09-27T07:49:53,823 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/kfdrc_production_vardict_wf.cwl' 2023-09-27T07:49:53,825 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/sb_multicnv_wf.cwl' 2023-09-27T07:49:53,826 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/config' 2023-09-27T07:49:53,828 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/main.nf' 2023-09-27T07:49:53,834 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/FGS.nf' 2023-09-27T07:49:53,835 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/QC_FLAG.nf' 2023-09-27T07:49:53,836 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/add_crossmapped_to_resmapped.nf' 2023-09-27T07:49:53,837 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/add_domain_positions.nf' 2023-09-27T07:49:53,838 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/align_avg_structs_pairwise.nf' 2023-09-27T07:49:53,839 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/antismash_gff.nf' 2023-09-27T07:49:53,841 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/antismash_summary.nf' 2023-09-27T07:49:53,842 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_averaged_structures.nf' 2023-09-27T07:49:53,843 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_averaged_unp_domains.nf' 2023-09-27T07:49:53,844 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_chopped_structs_unp_domains.nf' 2023-09-27T07:49:53,845 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_chopped_structures_unp_domains.nf' 2023-09-27T07:49:53,847 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/bam_index.nf' 2023-09-27T07:49:53,848 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/calc_chunking_number.nf' 2023-09-27T07:49:53,849 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/carveme.nf' 2023-09-27T07:49:53,850 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/carveme_files_to_folder.nf' 2023-09-27T07:49:53,852 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/cat.nf' 2023-09-27T07:49:53,853 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/cat_models.nf' 2023-09-27T07:49:53,854 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/check_alignment_scores.nf' 2023-09-27T07:49:53,855 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/check_threshold_step.nf' 2023-09-27T07:49:53,857 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/check_value.nf' 2023-09-27T07:49:53,858 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chinking_SC_fasta_nucleotide.nf' 2023-09-27T07:49:53,859 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chinking_fasta_nucleotide.nf' 2023-09-27T07:49:53,860 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chinking_fasta_proteins.nf' 2023-09-27T07:49:53,862 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chop_structs.nf' 2023-09-27T07:49:53,863 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chunking_fasta.nf' 2023-09-27T07:49:53,864 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chunking_tsv.nf' 2023-09-27T07:49:53,865 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/classifications_to_otu_counts.nf' 2023-09-27T07:49:53,866 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/clean_classification.nf' 2023-09-27T07:49:53,867 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/clean_fasta_headers.nf' 2023-09-27T07:49:53,869 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/clean_headers.nf' 2023-09-27T07:49:53,870 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/cmsearch.nf' 2023-09-27T07:49:53,871 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/collect_lost_instances.nf' 2023-09-27T07:49:53,873 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/combine.nf' 2023-09-27T07:49:53,874 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/combine_ips.nf' 2023-09-27T07:49:53,875 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/combine_trimmed.nf' 2023-09-27T07:49:53,876 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compare_instances_CATH_Pfam.nf' 2023-09-27T07:49:53,877 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress.nf' 2023-09-27T07:49:53,879 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress_carveme.nf' 2023-09-27T07:49:53,880 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress_mapseq.nf' 2023-09-27T07:49:53,881 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress_prodigal.nf' 2023-09-27T07:49:53,882 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compression.nf' 2023-09-27T07:49:53,883 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compression_func_ann.nf' 2023-09-27T07:49:53,885 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/conversion.nf' 2023-09-27T07:49:53,886 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/convert_trimmed_reads_to_fasta.nf' 2023-09-27T07:49:53,887 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/copy_avg_dom.nf' 2023-09-27T07:49:53,888 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_ITS_seqs.nf' 2023-09-27T07:49:53,889 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_cds.nf' 2023-09-27T07:49:53,890 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_lines_mapseq.nf' 2023-09-27T07:49:53,892 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_lsu_fasta.nf' 2023-09-27T07:49:53,893 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_masked_fasta.nf' 2023-09-27T07:49:53,894 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_overlapped_reads.nf' 2023-09-27T07:49:53,895 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_processed_reads.nf' 2023-09-27T07:49:53,896 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_reads.nf' 2023-09-27T07:49:53,898 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_reads_after_filtering.nf' 2023-09-27T07:49:53,899 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_ssu_fasta.nf' 2023-09-27T07:49:53,900 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_submitted_reads.nf' 2023-09-27T07:49:53,901 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_submitted_reads_single.nf' 2023-09-27T07:49:53,902 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/counts_to_hdf5.nf' 2023-09-27T07:49:53,903 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/counts_to_json.nf' 2023-09-27T07:49:53,904 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/create_csv_gp.nf' 2023-09-27T07:49:53,906 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/create_csv_kp.nf' 2023-09-27T07:49:53,907 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/create_new_parameters.nf' 2023-09-27T07:49:53,908 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/crossmapping_CATH2Pfam.nf' 2023-09-27T07:49:53,909 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/crossmapping_Pfam2CATH.nf' 2023-09-27T07:49:53,910 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/diamond_run.nf' 2023-09-27T07:49:53,911 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/eggnog_annotation.nf' 2023-09-27T07:49:53,912 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/eggnog_homology_searches.nf' 2023-09-27T07:49:53,914 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/expressiontool_bam_index.nf' 2023-09-27T07:49:53,915 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_coords.nf' 2023-09-27T07:49:53,916 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_sequences.nf' 2023-09-27T07:49:53,917 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_subunits.nf' 2023-09-27T07:49:53,918 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_subunits_coords.nf' 2023-09-27T07:49:53,920 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fasta_index.nf' 2023-09-27T07:49:53,921 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fastqc.nf' 2023-09-27T07:49:53,922 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fastqc_files_to_folder.nf' 2023-09-27T07:49:53,923 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_cath_structures.nf' 2023-09-27T07:49:53,924 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_contigs_antismash.nf' 2023-09-27T07:49:53,926 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_paired.nf' 2023-09-27T07:49:53,927 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_pfam_structures.nf' 2023-09-27T07:49:53,928 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fix_embl_and_gbk.nf' 2023-09-27T07:49:53,929 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fix_geneclusters_txt.nf' 2023-09-27T07:49:53,930 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/folder_compression.nf' 2023-09-27T07:49:53,931 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/format_core_list.nf' 2023-09-27T07:49:53,932 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/functional_stats.nf' 2023-09-27T07:49:53,934 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gather_domain_like.nf' 2023-09-27T07:49:53,935 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gather_failed_domains.nf' 2023-09-27T07:49:53,936 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gemstats.nf' 2023-09-27T07:49:53,937 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/genome_properties.nf' 2023-09-27T07:49:53,938 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/get_coords.nf' 2023-09-27T07:49:53,939 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/get_family_ids.nf' 2023-09-27T07:49:53,940 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/get_ncrnas.nf' 2023-09-27T07:49:53,942 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gff.nf' 2023-09-27T07:49:53,943 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/go_summary.nf' 2023-09-27T07:49:53,944 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip.nf' 2023-09-27T07:49:53,945 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_LSU.nf' 2023-09-27T07:49:53,946 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_SSU.nf' 2023-09-27T07:49:53,948 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_files.nf' 2023-09-27T07:49:53,949 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_masked_ITS.nf' 2023-09-27T07:49:53,950 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzipped_embl.nf' 2023-09-27T07:49:53,951 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzipped_gbk.nf' 2023-09-27T07:49:53,952 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hashsum.nf' 2023-09-27T07:49:53,953 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hashsum_paired.nf' 2023-09-27T07:49:53,954 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hashsum_single.nf' 2023-09-27T07:49:53,956 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/header_addition.nf' 2023-09-27T07:49:53,957 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hmmsearch.nf' 2023-09-27T07:49:53,958 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/index_reads.nf' 2023-09-27T07:49:53,959 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/interproscan.nf' 2023-09-27T07:49:53,961 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/join.nf' 2023-09-27T07:49:53,962 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/kegg_pathways.nf' 2023-09-27T07:49:53,963 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/kofamscan.nf' 2023-09-27T07:49:53,964 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/length_filter.nf' 2023-09-27T07:49:53,965 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/make_tab_sep.nf' 2023-09-27T07:49:53,967 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/mapseq.nf' 2023-09-27T07:49:53,968 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/mask_for_ITS.nf' 2023-09-27T07:49:53,969 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/memote_files_to_folder.nf' 2023-09-27T07:49:53,970 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/memote_report_snapshot.nf' 2023-09-27T07:49:53,971 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/memote_run.nf' 2023-09-27T07:49:53,972 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/motus_classification.nf' 2023-09-27T07:49:53,973 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_antismash_summary_to_pathways_systems_folder.nf' 2023-09-27T07:49:53,974 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_to_functional_annotation_folder.nf' 2023-09-27T07:49:53,976 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_to_pathways_systems_folder.nf' 2023-09-27T07:49:53,977 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_to_seq_cat_folder.nf' 2023-09-27T07:49:53,978 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/ngtax.nf' 2023-09-27T07:49:53,979 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/ngtax_files_to_folder.nf' 2023-09-27T07:49:53,980 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/ngtax_to_tsv_fasta.nf' 2023-09-27T07:49:53,982 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/no_tax_file_flag.nf' 2023-09-27T07:49:53,983 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/overlap_reads.nf' 2023-09-27T07:49:53,984 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/pairwise_align_avg_structs.nf' 2023-09-27T07:49:53,985 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/parsing_hmmscan.nf' 2023-09-27T07:49:53,986 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/per_dom_instance.nf' 2023-09-27T07:49:53,987 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/per_unp_dom_instance.nf' 2023-09-27T07:49:53,988 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/pfam.nf' 2023-09-27T07:49:53,989 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/phyloseq_files_to_folder.nf' 2023-09-27T07:49:53,991 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/picrust2.nf' 2023-09-27T07:49:53,992 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/picrust_files_to_folder.nf' 2023-09-27T07:49:53,993 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/pilon.nf' 2023-09-27T07:49:53,994 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/post_processing.nf' 2023-09-27T07:49:53,995 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/prodigal.nf' 2023-09-27T07:49:53,997 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/prodigal_files_to_folder.nf' 2023-09-27T07:49:53,998 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/qc_stats.nf' 2023-09-27T07:49:53,999 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/readmapping_pilon.nf' 2023-09-27T07:49:54,000 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/reads_to_folder.nf' 2023-09-27T07:49:54,001 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/reformat_coords.nf' 2023-09-27T07:49:54,002 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/remove_overlaps.nf' 2023-09-27T07:49:54,003 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/rename_contigs.nf' 2023-09-27T07:49:54,004 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/rename_geneclusters.nf' 2023-09-27T07:49:54,005 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/rename_ncrnas.nf' 2023-09-27T07:49:54,007 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/resmapping_for_CATH_PDB2UP.nf' 2023-09-27T07:49:54,008 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/resmapping_for_Pfam_UP2PDB.nf' 2023-09-27T07:49:54,009 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_antismash_in_folder.nf' 2023-09-27T07:49:54,010 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_its_dir.nf' 2023-09-27T07:49:54,011 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_output_dir.nf' 2023-09-27T07:49:54,012 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_seq_dir.nf' 2023-09-27T07:49:54,013 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_tax_dir.nf' 2023-09-27T07:49:54,015 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_antismash.nf' 2023-09-27T07:49:54,016 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_concatenate_deoverlapped_matches.nf' 2023-09-27T07:49:54,017 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_concatenate_matches.nf' 2023-09-27T07:49:54,018 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_quality_control_filtering.nf' 2023-09-27T07:49:54,019 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/sam_to_sorted_bam.nf' 2023-09-27T07:49:54,020 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/smetana.nf' 2023-09-27T07:49:54,021 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/sorting.nf' 2023-09-27T07:49:54,023 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/split_fasta.nf' 2023-09-27T07:49:54,024 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/split_seqs.nf' 2023-09-27T07:49:54,025 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/suppress_tax.nf' 2023-09-27T07:49:54,026 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/tab_modification.nf' 2023-09-27T07:49:54,027 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/tohdt.nf' 2023-09-27T07:49:54,029 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_empty_fasta.nf' 2023-09-27T07:49:54,030 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_file_flag.nf' 2023-09-27T07:49:54,031 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_no_antismash_flag.nf' 2023-09-27T07:49:54,032 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_no_cds_flag.nf' 2023-09-27T07:49:54,033 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/trim_quality_control.nf' 2023-09-27T07:49:54,034 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_embl.nf' 2023-09-27T07:49:54,035 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_gbk.nf' 2023-09-27T07:49:54,036 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_geneclusters_txt.nf' 2023-09-27T07:49:54,038 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_seed_orthologs.nf' 2023-09-27T07:49:54,039 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unzip.nf' 2023-09-27T07:49:54,040 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unzip_merged_reads.nf' 2023-09-27T07:49:54,041 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unzip_single_reads.nf' 2023-09-27T07:49:54,042 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/vcf_compress.nf' 2023-09-27T07:49:54,043 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/visualize_otu_counts.nf' 2023-09-27T07:49:54,044 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/write_summaries.nf' 2023-09-27T07:49:54,047 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/ITS.nf' 2023-09-27T07:49:54,048 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/after_qc.nf' 2023-09-27T07:49:54,050 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/antismash.nf' 2023-09-27T07:49:54,051 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/avg_unp_domains.nf' 2023-09-27T07:49:54,052 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/before_qc.nf' 2023-09-27T07:49:54,053 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cath_domain_instances.nf' 2023-09-27T07:49:54,054 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cgc.nf' 2023-09-27T07:49:54,056 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/change_formats_and_names.nf' 2023-09-27T07:49:54,057 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_for_CATH2Pfam.nf' 2023-09-27T07:49:54,058 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_for_Pfam2CATH.nf' 2023-09-27T07:49:54,059 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_for_core.nf' 2023-09-27T07:49:54,060 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_from_list.nf' 2023-09-27T07:49:54,062 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chunking.nf' 2023-09-27T07:49:54,063 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chunking_final.nf' 2023-09-27T07:49:54,064 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/classify_LSUs.nf' 2023-09-27T07:49:54,065 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/classify_SSUs.nf' 2023-09-27T07:49:54,067 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cmsearch_assembly.nf' 2023-09-27T07:49:54,068 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cmsearch_raw_data.nf' 2023-09-27T07:49:54,069 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/combined_gene_caller.nf' 2023-09-27T07:49:54,070 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/diamond.nf' 2023-09-27T07:49:54,071 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/eggnog.nf' 2023-09-27T07:49:54,072 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/filtering.nf' 2023-09-27T07:49:54,073 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/find_ribosomal_ncRNAs.nf' 2023-09-27T07:49:54,075 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/folder_functional_annotation.nf' 2023-09-27T07:49:54,076 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/functional_annotation.nf' 2023-09-27T07:49:54,077 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/functional_annotation_and_post_processing.nf' 2023-09-27T07:49:54,078 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/motus_taxonomy.nf' 2023-09-27T07:49:54,079 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/no_antismash_subwf.nf' 2023-09-27T07:49:54,081 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/other_ncrnas.nf' 2023-09-27T07:49:54,082 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/overlap_reads.nf' 2023-09-27T07:49:54,083 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/pathways.nf' 2023-09-27T07:49:54,084 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/pfam_domain_instances.nf' 2023-09-27T07:49:54,085 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/post_processing_uniref90.nf' 2023-09-27T07:49:54,087 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/resmapping_cath_structs.nf' 2023-09-27T07:49:54,088 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/resmapping_pfam_structs.nf' 2023-09-27T07:49:54,089 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/rna_prediction.nf' 2023-09-27T07:49:54,091 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_IPS.nf' 2023-09-27T07:49:54,092 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_antismash.nf' 2023-09-27T07:49:54,093 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_hmmer.nf' 2023-09-27T07:49:54,094 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_itsonedb.nf' 2023-09-27T07:49:54,096 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/run_unite.nf' 2023-09-27T07:49:54,097 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/trimming.nf' 2023-09-27T07:49:54,098 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/unmapped_from_cath.nf' 2023-09-27T07:49:54,099 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/unmapped_from_pfam.nf' 2023-09-27T07:49:54,100 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/write_summaries.nf' 2023-09-27T07:49:54,103 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/cnvkit_single_sample_wf.cwl' 2023-09-27T07:49:54,104 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/control-freec-germline.cwl' 2023-09-27T07:49:54,105 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_cnv_caller_wes_wf.cwl' 2023-09-27T07:49:54,106 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_cnvkit_batch_wf.cwl' 2023-09-27T07:49:54,107 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_cnvkit_plus_theta2.cwl' 2023-09-27T07:49:54,109 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_combined_somatic_wgs_cnv_wf.cwl' 2023-09-27T07:49:54,110 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_controlfreec_cnv.cwl' 2023-09-27T07:49:54,112 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_lancet_wf.cwl' 2023-09-27T07:49:54,113 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_mutect2_wf.cwl' 2023-09-27T07:49:54,115 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_production_WES_somatic_variant_cnv_wf.cwl' 2023-09-27T07:49:54,117 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_production_WGS_somatic_variant_cnv.cwl' 2023-09-27T07:49:54,119 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_somatic_WES_wf.cwl' 2023-09-27T07:49:54,121 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_somatic_caller_workflow.cwl' 2023-09-27T07:49:54,122 adding 'janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflows-deprecated/kfdrc_vardict_wf.cwl' 2023-09-27T07:49:54,125 adding 'janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/.gitkeep' 2023-09-27T07:49:54,126 adding 'janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/featurecounts.cwl' 2023-09-27T07:49:54,128 adding 'janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/kallisto/kallisto_index.cwl' 2023-09-27T07:49:54,130 adding 'janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/kallisto/kallisto_quant.cwl' 2023-09-27T07:49:54,132 adding 'janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/star/star_align.cwl' 2023-09-27T07:49:54,133 adding 'janis_core/tests/data/cwl/workflows/m-unlock/RNAseq/star/star_index.cwl' 2023-09-27T07:49:54,135 adding 'janis_core/tests/data/cwl/workflows/m-unlock/aragorn/aragorn.cwl' 2023-09-27T07:49:54,136 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bash/compress.cwl' 2023-09-27T07:49:54,138 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bash/compress_directory.cwl' 2023-09-27T07:49:54,139 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bash/concatenate.cwl' 2023-09-27T07:49:54,140 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bash/decompress.cwl' 2023-09-27T07:49:54,141 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bash/grep_count.cwl' 2023-09-27T07:49:54,143 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bash/pigz.cwl' 2023-09-27T07:49:54,144 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bash/rename.cwl' 2023-09-27T07:49:54,146 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bbmap/bbduk_filter.cwl' 2023-09-27T07:49:54,147 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bbmap/bbduk_rrna-filter.cwl' 2023-09-27T07:49:54,148 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bbmap/bbmap.cwl' 2023-09-27T07:49:54,150 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bbmap/bbmap_filter-reads.cwl' 2023-09-27T07:49:54,151 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bbmap/prepare_fasta_db.cwl' 2023-09-27T07:49:54,154 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bowtie2/bowtie2_align.cwl' 2023-09-27T07:49:54,155 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bowtie2/bowtie2_align_simple.cwl' 2023-09-27T07:49:54,157 adding 'janis_core/tests/data/cwl/workflows/m-unlock/bowtie2/bowtie2_index.cwl' 2023-09-27T07:49:54,159 adding 'janis_core/tests/data/cwl/workflows/m-unlock/busco/busco.cwl' 2023-09-27T07:49:54,160 adding 'janis_core/tests/data/cwl/workflows/m-unlock/carveme/GEMstats.cwl' 2023-09-27T07:49:54,161 adding 'janis_core/tests/data/cwl/workflows/m-unlock/carveme/carveme.cwl' 2023-09-27T07:49:54,163 adding 'janis_core/tests/data/cwl/workflows/m-unlock/checkm/checkm_lineagewf.cwl' 2023-09-27T07:49:54,165 adding 'janis_core/tests/data/cwl/workflows/m-unlock/clustalo/clustalo.cwl' 2023-09-27T07:49:54,166 adding 'janis_core/tests/data/cwl/workflows/m-unlock/das_tool/das_tool.cwl' 2023-09-27T07:49:54,168 adding 'janis_core/tests/data/cwl/workflows/m-unlock/das_tool/fasta_to_contig2bin.cwl' 2023-09-27T07:49:54,170 adding 'janis_core/tests/data/cwl/workflows/m-unlock/diamond/diamond.cwl' 2023-09-27T07:49:54,171 adding 'janis_core/tests/data/cwl/workflows/m-unlock/diamond/view.cwl' 2023-09-27T07:49:54,172 adding 'janis_core/tests/data/cwl/workflows/m-unlock/ena/ena_wget.cwl' 2023-09-27T07:49:54,174 adding 'janis_core/tests/data/cwl/workflows/m-unlock/eukrep/eukrep.cwl' 2023-09-27T07:49:54,176 adding 'janis_core/tests/data/cwl/workflows/m-unlock/expressions/array_to_file.cwl' 2023-09-27T07:49:54,177 adding 'janis_core/tests/data/cwl/workflows/m-unlock/expressions/files_to_folder.cwl' 2023-09-27T07:49:54,178 adding 'janis_core/tests/data/cwl/workflows/m-unlock/expressions/folder_file_regex.cwl' 2023-09-27T07:49:54,179 adding 'janis_core/tests/data/cwl/workflows/m-unlock/expressions/folder_to_files.cwl' 2023-09-27T07:49:54,180 adding 'janis_core/tests/data/cwl/workflows/m-unlock/expressions/merge_dir_arrays.cwl' 2023-09-27T07:49:54,182 adding 'janis_core/tests/data/cwl/workflows/m-unlock/expressions/merge_file_arrays.cwl' 2023-09-27T07:49:54,184 adding 'janis_core/tests/data/cwl/workflows/m-unlock/fastp/fastp.cwl' 2023-09-27T07:49:54,185 adding 'janis_core/tests/data/cwl/workflows/m-unlock/fastq/fastq_to_fasta.cwl' 2023-09-27T07:49:54,187 adding 'janis_core/tests/data/cwl/workflows/m-unlock/fastqc/fastqc.cwl' 2023-09-27T07:49:54,189 adding 'janis_core/tests/data/cwl/workflows/m-unlock/filtlong/filtlong.cwl' 2023-09-27T07:49:54,191 adding 'janis_core/tests/data/cwl/workflows/m-unlock/flye/flye.cwl' 2023-09-27T07:49:54,193 adding 'janis_core/tests/data/cwl/workflows/m-unlock/gtdbtk/gtdbtk_classify_wf.cwl' 2023-09-27T07:49:54,195 adding 'janis_core/tests/data/cwl/workflows/m-unlock/gunc/gunc.cwl' 2023-09-27T07:49:54,196 adding 'janis_core/tests/data/cwl/workflows/m-unlock/guppy/guppy.cwl' 2023-09-27T07:49:54,198 adding 'janis_core/tests/data/cwl/workflows/m-unlock/humann/humann.cwl' 2023-09-27T07:49:54,200 adding 'janis_core/tests/data/cwl/workflows/m-unlock/irods/irods_hdt.cwl' 2023-09-27T07:49:54,201 adding 'janis_core/tests/data/cwl/workflows/m-unlock/irods/irods_manager.cwl' 2023-09-27T07:49:54,203 adding 'janis_core/tests/data/cwl/workflows/m-unlock/kraken2/kraken2-build.cwl' 2023-09-27T07:49:54,205 adding 'janis_core/tests/data/cwl/workflows/m-unlock/kraken2/kraken2.cwl' 2023-09-27T07:49:54,206 adding 'janis_core/tests/data/cwl/workflows/m-unlock/krona/krona.cwl' 2023-09-27T07:49:54,208 adding 'janis_core/tests/data/cwl/workflows/m-unlock/longqc/longqc.cwl' 2023-09-27T07:49:54,210 adding 'janis_core/tests/data/cwl/workflows/m-unlock/maxbin2/maxbin2.cwl' 2023-09-27T07:49:54,212 adding 'janis_core/tests/data/cwl/workflows/m-unlock/medaka/medaka.cwl' 2023-09-27T07:49:54,213 adding 'janis_core/tests/data/cwl/workflows/m-unlock/medaka/medaka_py.cwl' 2023-09-27T07:49:54,215 adding 'janis_core/tests/data/cwl/workflows/m-unlock/memote/memote.cwl' 2023-09-27T07:49:54,217 adding 'janis_core/tests/data/cwl/workflows/m-unlock/merge/merge.cwl' 2023-09-27T07:49:54,219 adding 'janis_core/tests/data/cwl/workflows/m-unlock/metabat2/aggregateBinDepths.cwl' 2023-09-27T07:49:54,220 adding 'janis_core/tests/data/cwl/workflows/m-unlock/metabat2/metabat2.cwl' 2023-09-27T07:49:54,221 adding 'janis_core/tests/data/cwl/workflows/m-unlock/metabat2/metabatContigDepths.cwl' 2023-09-27T07:49:54,223 adding 'janis_core/tests/data/cwl/workflows/m-unlock/metagenomics/assembly_bins_readstats.cwl' 2023-09-27T07:49:54,224 adding 'janis_core/tests/data/cwl/workflows/m-unlock/metagenomics/bins_summary.cwl' 2023-09-27T07:49:54,226 adding 'janis_core/tests/data/cwl/workflows/m-unlock/metagenomics/get_unbinned_contigs.cwl' 2023-09-27T07:49:54,227 adding 'janis_core/tests/data/cwl/workflows/m-unlock/minimap2/minimap2.cwl' 2023-09-27T07:49:54,229 adding 'janis_core/tests/data/cwl/workflows/m-unlock/minimap2/minimap2_to_fastq.cwl' 2023-09-27T07:49:54,230 adding 'janis_core/tests/data/cwl/workflows/m-unlock/minimap2/minimap2_to_sorted-bam.cwl' 2023-09-27T07:49:54,231 adding 'janis_core/tests/data/cwl/workflows/m-unlock/minionqc/minionqc.cwl' 2023-09-27T07:49:54,233 adding 'janis_core/tests/data/cwl/workflows/m-unlock/multiqc/multiqc.cwl' 2023-09-27T07:49:54,235 adding 'janis_core/tests/data/cwl/workflows/m-unlock/nanoqc/nanoqc.cwl' 2023-09-27T07:49:54,237 adding 'janis_core/tests/data/cwl/workflows/m-unlock/ngtax/ngtax.cwl' 2023-09-27T07:49:54,238 adding 'janis_core/tests/data/cwl/workflows/m-unlock/ngtax/ngtax_demultiplexing.cwl' 2023-09-27T07:49:54,239 adding 'janis_core/tests/data/cwl/workflows/m-unlock/ngtax/ngtax_to_biom.cwl' 2023-09-27T07:49:54,243 adding 'janis_core/tests/data/cwl/workflows/m-unlock/ngtax/ngtax_to_tsv-fasta.cwl' 2023-09-27T07:49:54,252 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_RNAseq_NonSpliced_packed.cwl' 2023-09-27T07:49:54,260 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_RNAseq_Spliced_packed.cwl' 2023-09-27T07:49:54,267 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_RNAseq_kallisto_packed.cwl' 2023-09-27T07:49:54,270 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_demultiplexing_packed.cwl' 2023-09-27T07:49:54,271 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_ena_annotation_packed.cwl' 2023-09-27T07:49:54,272 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_genomesync_packed.cwl' 2023-09-27T07:49:54,281 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_illumina_assembly_packed.cwl' 2023-09-27T07:49:54,287 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_illumina_quality_packed.cwl' 2023-09-27T07:49:54,290 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_indexbuilder_packed.cwl' 2023-09-27T07:49:54,295 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_longread_quality_packed.cwl' 2023-09-27T07:49:54,299 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_GEM_packed.cwl' 2023-09-27T07:49:54,324 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_assembly_packed.cwl' 2023-09-27T07:49:54,336 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_binning_packed.cwl' 2023-09-27T07:49:54,338 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_packed.cwl' 2023-09-27T07:49:54,346 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_metagenomics_read_annotation_packed.cwl' 2023-09-27T07:49:54,349 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_microbial_packed.cwl' 2023-09-27T07:49:54,351 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_mock_ngtax_packed.cwl' 2023-09-27T07:49:54,353 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_nanopore_packed.cwl' 2023-09-27T07:49:54,355 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_ngtax_packed.cwl' 2023-09-27T07:49:54,358 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_ngtax_picrust2_packed.cwl' 2023-09-27T07:49:54,361 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_pilon_mapping_packed.cwl' 2023-09-27T07:49:54,364 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_prepare_fasta_db_packed.cwl' 2023-09-27T07:49:54,366 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_samsa2_packed.cwl' 2023-09-27T07:49:54,369 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_sapp_microbes_packed.cwl' 2023-09-27T07:49:54,371 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_sapp_others_packed.cwl' 2023-09-27T07:49:54,372 adding 'janis_core/tests/data/cwl/workflows/m-unlock/packed/workflow_toHDT_compression_packed.cwl' 2023-09-27T07:49:54,374 adding 'janis_core/tests/data/cwl/workflows/m-unlock/picrust2/picrust2_pipeline.cwl' 2023-09-27T07:49:54,375 adding 'janis_core/tests/data/cwl/workflows/m-unlock/picrust2/picrust_to_biom.cwl' 2023-09-27T07:49:54,377 adding 'janis_core/tests/data/cwl/workflows/m-unlock/pilon/pilon.cwl' 2023-09-27T07:49:54,379 adding 'janis_core/tests/data/cwl/workflows/m-unlock/prodigal/prodigal.cwl' 2023-09-27T07:49:54,381 adding 'janis_core/tests/data/cwl/workflows/m-unlock/pycoqc/pycoqc.cwl' 2023-09-27T07:49:54,383 adding 'janis_core/tests/data/cwl/workflows/m-unlock/quast/metaquast.cwl' 2023-09-27T07:49:54,384 adding 'janis_core/tests/data/cwl/workflows/m-unlock/quast/quast.cwl' 2023-09-27T07:49:54,386 adding 'janis_core/tests/data/cwl/workflows/m-unlock/resfinder/resfinder.cwl' 2023-09-27T07:49:54,387 adding 'janis_core/tests/data/cwl/workflows/m-unlock/samsa2/convert.cwl' 2023-09-27T07:49:54,389 adding 'janis_core/tests/data/cwl/workflows/m-unlock/samtools/expression_bam_index.cwl' 2023-09-27T07:49:54,390 adding 'janis_core/tests/data/cwl/workflows/m-unlock/samtools/merge-sorted-bam.cwl' 2023-09-27T07:49:54,392 adding 'janis_core/tests/data/cwl/workflows/m-unlock/samtools/sam_to_fastq_PE.cwl' 2023-09-27T07:49:54,393 adding 'janis_core/tests/data/cwl/workflows/m-unlock/samtools/sam_to_fastq_SE.cwl' 2023-09-27T07:49:54,394 adding 'janis_core/tests/data/cwl/workflows/m-unlock/samtools/sam_to_sorted-bam.cwl' 2023-09-27T07:49:54,396 adding 'janis_core/tests/data/cwl/workflows/m-unlock/samtools/sam_to_unmapped_fastq_SE.cwl' 2023-09-27T07:49:54,397 adding 'janis_core/tests/data/cwl/workflows/m-unlock/samtools/samtools_flagstat.cwl' 2023-09-27T07:49:54,398 adding 'janis_core/tests/data/cwl/workflows/m-unlock/samtools/samtools_idxstats.cwl' 2023-09-27T07:49:54,399 adding 'janis_core/tests/data/cwl/workflows/m-unlock/samtools/samtools_index.cwl' 2023-09-27T07:49:54,401 adding 'janis_core/tests/data/cwl/workflows/m-unlock/sapp/conversion.cwl' 2023-09-27T07:49:54,403 adding 'janis_core/tests/data/cwl/workflows/m-unlock/sapp/conversion_rdf2fasta.cwl' 2023-09-27T07:49:54,404 adding 'janis_core/tests/data/cwl/workflows/m-unlock/sapp/conversion_rdf2gtf.cwl' 2023-09-27T07:49:54,405 adding 'janis_core/tests/data/cwl/workflows/m-unlock/sapp/crt.cwl' 2023-09-27T07:49:54,407 adding 'janis_core/tests/data/cwl/workflows/m-unlock/sapp/infernal.cwl' 2023-09-27T07:49:54,408 adding 'janis_core/tests/data/cwl/workflows/m-unlock/sapp/interproscan.cwl' 2023-09-27T07:49:54,409 adding 'janis_core/tests/data/cwl/workflows/m-unlock/sapp/kofamscan.cwl' 2023-09-27T07:49:54,410 adding 'janis_core/tests/data/cwl/workflows/m-unlock/sapp/prodigal.cwl' 2023-09-27T07:49:54,412 adding 'janis_core/tests/data/cwl/workflows/m-unlock/sapp/toHDT.cwl' 2023-09-27T07:49:54,414 adding 'janis_core/tests/data/cwl/workflows/m-unlock/semibin/semibin_rename_bins.cwl' 2023-09-27T07:49:54,415 adding 'janis_core/tests/data/cwl/workflows/m-unlock/semibin/semibin_single_easy_bin.cwl' 2023-09-27T07:49:54,417 adding 'janis_core/tests/data/cwl/workflows/m-unlock/smetana/smetana.cwl' 2023-09-27T07:49:54,419 adding 'janis_core/tests/data/cwl/workflows/m-unlock/spades/spades.cwl' 2023-09-27T07:49:54,421 adding 'janis_core/tests/data/cwl/workflows/m-unlock/stats/raw_n50.cwl' 2023-09-27T07:49:54,422 adding 'janis_core/tests/data/cwl/workflows/m-unlock/stats/seqinfo.cwl' 2023-09-27T07:49:54,424 adding 'janis_core/tests/data/cwl/workflows/m-unlock/workflows/demultiplexing.cwl' 2023-09-27T07:49:54,425 adding 'janis_core/tests/data/cwl/workflows/m-unlock/workflows/metagenomics_GEM.cwl' 2023-09-27T07:49:54,426 adding 'janis_core/tests/data/cwl/workflows/m-unlock/workflows/mock_ngtax.cwl' 2023-09-27T07:49:54,428 adding 'janis_core/tests/data/cwl/workflows/m-unlock/workflows/ngtax.cwl' 2023-09-27T07:49:54,429 adding 'janis_core/tests/data/cwl/workflows/m-unlock/workflows/ngtax_picrust2.cwl' 2023-09-27T07:49:54,431 adding 'janis_core/tests/data/cwl/workflows/m-unlock/workflows/pilon_mapping.cwl' 2023-09-27T07:49:54,432 adding 'janis_core/tests/data/cwl/workflows/m-unlock/workflows/sapp_microbes.cwl' 2023-09-27T07:49:54,433 adding 'janis_core/tests/data/cwl/workflows/m-unlock/workflows/toHDT_compression.cwl' 2023-09-27T07:49:54,435 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/workflow.cwl' 2023-09-27T07:49:54,436 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/workflow.yaml' 2023-09-27T07:49:54,438 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/workflow_idxs.yaml' 2023-09-27T07:49:54,440 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/batch_parser.cwl' 2023-09-27T07:49:54,441 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bedops_union.cwl' 2023-09-27T07:49:54,442 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bgzip.cwl' 2023-09-27T07:49:54,443 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bundle_secondaryfiles.cwl' 2023-09-27T07:49:54,444 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bwa_index.cwl' 2023-09-27T07:49:54,445 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bwa_mem_paired.cwl' 2023-09-27T07:49:54,446 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/bwa_mem_unpaired.cwl' 2023-09-27T07:49:54,448 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/codex.cwl' 2023-09-27T07:49:54,449 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/codex_filter.cwl' 2023-09-27T07:49:54,450 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/collapse.cwl' 2023-09-27T07:49:54,451 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/exome_depth.cwl' 2023-09-27T07:49:54,452 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/exome_depth_filter.cwl' 2023-09-27T07:49:54,453 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/fastp.cwl' 2023-09-27T07:49:54,455 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/fastqc.cwl' 2023-09-27T07:49:54,456 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/gridss.cwl' 2023-09-27T07:49:54,457 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/gridss_filter.cwl' 2023-09-27T07:49:54,458 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/gunzip.cwl' 2023-09-27T07:49:54,459 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/manta.cwl' 2023-09-27T07:49:54,460 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/manta_filter.cwl' 2023-09-27T07:49:54,462 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/merge_all.cwl' 2023-09-27T07:49:54,463 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/picard_markduplicates.cwl' 2023-09-27T07:49:54,464 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_faidx.cwl' 2023-09-27T07:49:54,465 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_index.cwl' 2023-09-27T07:49:54,467 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_merge.cwl' 2023-09-27T07:49:54,468 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_sort.cwl' 2023-09-27T07:49:54,469 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_view.cwl' 2023-09-27T07:49:54,470 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/samtools_view_sam2bam.cwl' 2023-09-27T07:49:54,471 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/structural_variants.cwl' 2023-09-27T07:49:54,472 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/svtools.cwl' 2023-09-27T07:49:54,473 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/tabix.cwl' 2023-09-27T07:49:54,475 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/bam_filtering.cwl' 2023-09-27T07:49:54,476 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/bwa_index.cwl' 2023-09-27T07:49:54,477 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/bwa_mem.cwl' 2023-09-27T07:49:54,478 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/cnv_codex.cwl' 2023-09-27T07:49:54,479 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/cnv_exome_depth.cwl' 2023-09-27T07:49:54,480 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/cnv_gridss.cwl' 2023-09-27T07:49:54,482 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/cnv_manta.cwl' 2023-09-27T07:49:54,483 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/final_filtering.cwl' 2023-09-27T07:49:54,484 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/indexing_bed.cwl' 2023-09-27T07:49:54,485 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/picard_markduplicates.cwl' 2023-09-27T07:49:54,486 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/samtools_sort.cwl' 2023-09-27T07:49:54,487 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/samtools_view_sam2bam.cwl' 2023-09-27T07:49:54,488 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_operations/subworkflows/trimmed_fastq.cwl' 2023-09-27T07:49:54,491 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/abstract_workflow/abstract_workflow.cwl' 2023-09-27T07:49:54,492 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/bam_filtering.cwl' 2023-09-27T07:49:54,494 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/bwa_index.cwl' 2023-09-27T07:49:54,495 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/bwa_mem.cwl' 2023-09-27T07:49:54,496 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/cnv_codex.cwl' 2023-09-27T07:49:54,498 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/cnv_exome_depth.cwl' 2023-09-27T07:49:54,499 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/cnv_gridss.cwl' 2023-09-27T07:49:54,500 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/cnv_manta.cwl' 2023-09-27T07:49:54,501 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/final_filtering.cwl' 2023-09-27T07:49:54,502 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/indexing_bed.cwl' 2023-09-27T07:49:54,504 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/indexing_bed.yaml' 2023-09-27T07:49:54,505 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/picard_markduplicates.cwl' 2023-09-27T07:49:54,506 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/samtools_sort.cwl' 2023-09-27T07:49:54,507 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/samtools_view_sam2bam.cwl' 2023-09-27T07:49:54,508 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/subworkflows/trimmed_fastq.cwl' 2023-09-27T07:49:54,510 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/batch_parser.cwl' 2023-09-27T07:49:54,511 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/bedops_union.cwl' 2023-09-27T07:49:54,512 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/bgzip.cwl' 2023-09-27T07:49:54,514 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/bundle_secondaryfiles.cwl' 2023-09-27T07:49:54,515 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_index.cwl' 2023-09-27T07:49:54,516 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_index_grace.cwl' 2023-09-27T07:49:54,517 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_mem_paired.cwl' 2023-09-27T07:49:54,518 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_mem_paired_grace.cwl' 2023-09-27T07:49:54,519 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_mem_unpaired.cwl' 2023-09-27T07:49:54,520 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/bwa_mem_unpaired_grace.cwl' 2023-09-27T07:49:54,522 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/codex.cwl' 2023-09-27T07:49:54,523 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/codex_filter.cwl' 2023-09-27T07:49:54,524 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/collapse.cwl' 2023-09-27T07:49:54,526 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/exome_depth.cwl' 2023-09-27T07:49:54,527 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/exome_depth_filter.cwl' 2023-09-27T07:49:54,528 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/fastp.cwl' 2023-09-27T07:49:54,529 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/fastqc.cwl' 2023-09-27T07:49:54,531 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/gridss.cwl' 2023-09-27T07:49:54,532 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/gridss_filter.cwl' 2023-09-27T07:49:54,533 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/gunzip.cwl' 2023-09-27T07:49:54,534 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/manta.cwl' 2023-09-27T07:49:54,535 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/manta_filter.cwl' 2023-09-27T07:49:54,537 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/merge_all.cwl' 2023-09-27T07:49:54,538 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/picard_markduplicates.cwl' 2023-09-27T07:49:54,539 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_faidx.cwl' 2023-09-27T07:49:54,540 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_index.cwl' 2023-09-27T07:49:54,541 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_merge.cwl' 2023-09-27T07:49:54,543 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_sort.cwl' 2023-09-27T07:49:54,544 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_view.cwl' 2023-09-27T07:49:54,545 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/samtools_view_sam2bam.cwl' 2023-09-27T07:49:54,546 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/structural_variants.cwl' 2023-09-27T07:49:54,548 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/svtools.cwl' 2023-09-27T07:49:54,549 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/tabix.cwl' 2023-09-27T07:49:54,550 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/tools_list.txt' 2023-09-27T07:49:54,552 adding 'janis_core/tests/data/cwl/workflows/structuralvariants/tools/unicycler.cwl' 2023-09-27T07:49:54,553 adding 'janis_core/tests/data/cwl/workflows/subworkflow_test/basic.cwl' 2023-09-27T07:49:54,554 adding 'janis_core/tests/data/cwl/workflows/subworkflow_test/main.cwl' 2023-09-27T07:49:54,556 adding 'janis_core/tests/data/cwl/workflows/subworkflow_test/mandatory_input_types.cwl' 2023-09-27T07:49:54,557 adding 'janis_core/tests/data/cwl/workflows/subworkflow_test/optional_input_types.cwl' 2023-09-27T07:49:54,558 adding 'janis_core/tests/data/cwl/workflows/subworkflow_test/subworkflow.cwl' 2023-09-27T07:49:54,560 adding 'janis_core/tests/data/galaxy/annotate-my-ids-wf.ga' 2023-09-27T07:49:54,561 adding 'janis_core/tests/data/galaxy/cutadapt_wf.ga' 2023-09-27T07:49:54,563 adding 'janis_core/tests/data/galaxy/fastqc_wf.ga' 2023-09-27T07:49:54,564 adding 'janis_core/tests/data/galaxy/goseq_wf.ga' 2023-09-27T07:49:54,565 adding 'janis_core/tests/data/galaxy/hisat2_wf.ga' 2023-09-27T07:49:54,567 adding 'janis_core/tests/data/galaxy/limma_voom_wf.ga' 2023-09-27T07:49:54,568 adding 'janis_core/tests/data/galaxy/nanoplot_wf.ga' 2023-09-27T07:49:54,570 adding 'janis_core/tests/data/galaxy/rna_seq_counts_to_genes.ga' 2023-09-27T07:49:54,572 adding 'janis_core/tests/data/galaxy/rna_seq_genes_to_pathways.ga' 2023-09-27T07:49:54,575 adding 'janis_core/tests/data/galaxy/rna_seq_reads_to_counts.ga' 2023-09-27T07:49:54,577 adding 'janis_core/tests/data/galaxy/unicycler_assembly.ga' 2023-09-27T07:49:54,579 adding 'janis_core/tests/data/galaxy/wf_abricate.ga' 2023-09-27T07:49:54,580 adding 'janis_core/tests/data/galaxy/wf_featurecounts.ga' 2023-09-27T07:49:54,581 adding 'janis_core/tests/data/galaxy/wf_mark_duplicates.ga' 2023-09-27T07:49:54,583 adding 'janis_core/tests/data/galaxy/wf_samtools_idxstats.ga' 2023-09-27T07:49:54,584 adding 'janis_core/tests/data/galaxy/abricate/.shed.yml' 2023-09-27T07:49:54,586 adding 'janis_core/tests/data/galaxy/abricate/abricate.xml' 2023-09-27T07:49:54,587 adding 'janis_core/tests/data/galaxy/abricate/abricate_list.xml' 2023-09-27T07:49:54,589 adding 'janis_core/tests/data/galaxy/abricate/abricate_summary.xml' 2023-09-27T07:49:54,590 adding 'janis_core/tests/data/galaxy/abricate/macros.xml' 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'janis_core/tests/data/galaxy/hisat2-6c19daec423d/tool_data_table_conf.xml.test' 2023-09-27T07:49:56,349 adding 'janis_core/tests/data/galaxy/hisat2-6c19daec423d/tool-data/hisat2_indexes.loc.sample' 2023-09-27T07:49:56,351 adding 'janis_core/tests/data/galaxy/nanoplot-edbb6c5028f5/.hg_archival.txt' 2023-09-27T07:49:56,353 adding 'janis_core/tests/data/galaxy/nanoplot-edbb6c5028f5/nanoplot.xml' 2023-09-27T07:49:56,355 adding 'janis_core/tests/data/galaxy/quast-675488238c96/macros.xml' 2023-09-27T07:49:56,359 adding 'janis_core/tests/data/galaxy/quast-675488238c96/quast.xml' 2023-09-27T07:49:56,362 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/.hg_archival.txt' 2023-09-27T07:49:56,364 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/ansi2html.sh' 2023-09-27T07:49:56,365 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/awk.xml' 2023-09-27T07:49:56,367 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/cat.xml' 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'janis_core/tests/data/galaxy/text_processing-d698c222f354/multijoin.xml' 2023-09-27T07:49:56,384 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/readme.rst' 2023-09-27T07:49:56,385 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/recurring_lines.xml' 2023-09-27T07:49:56,387 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/replace_text_in_column.xml' 2023-09-27T07:49:56,388 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/replace_text_in_line.xml' 2023-09-27T07:49:56,390 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/sed.xml' 2023-09-27T07:49:56,392 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/sort-header' 2023-09-27T07:49:56,393 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/sort.xml' 2023-09-27T07:49:56,395 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/sort_rows.xml' 2023-09-27T07:49:56,396 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/sorted_uniq.xml' 2023-09-27T07:49:56,398 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/tac.xml' 2023-09-27T07:49:56,399 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/tail.xml' 2023-09-27T07:49:56,400 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/unfold_column.py' 2023-09-27T07:49:56,401 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/unfold_column.xml' 2023-09-27T07:49:56,403 adding 'janis_core/tests/data/galaxy/text_processing-d698c222f354/unsorted_uniq.xml' 2023-09-27T07:49:56,425 adding 'janis_core/tests/data/janis/test_codetool.py' 2023-09-27T07:49:56,435 adding 'janis_core/tests/data/janis/simple/workflow.py' 2023-09-27T07:49:56,475 adding 'janis_core/tests/data/janis/simple/scripts/multiqc_multiqc_config' 2023-09-27T07:49:56,773 adding 'janis_core/tests/data/janis/simple/tools/fastqc.py' 2023-09-27T07:49:56,775 adding 'janis_core/tests/data/janis/simple/tools/multiqc.py' 2023-09-27T07:49:56,776 adding 'janis_core/tests/data/janis/simple/tools/prokka.py' 2023-09-27T07:49:56,778 adding 'janis_core/tests/data/janis/simple/tools/quast.py' 2023-09-27T07:49:56,781 adding 'janis_core/tests/data/janis/simple/tools/unicycler.py' 2023-09-27T07:49:56,783 adding 'janis_core/tests/data/janis/simple_truncated/scripts/multiqc_multiqc_config' 2023-09-27T07:49:56,785 adding 'janis_core/tests/data/janis/simple_truncated/tools/multiqc.py' 2023-09-27T07:49:56,786 adding 'janis_core/tests/data/janis/simple_truncated/tools/prokka.py' 2023-09-27T07:49:56,788 adding 'janis_core/tests/data/janis/simple_truncated/tools/quast.py' 2023-09-27T07:49:56,790 adding 'janis_core/tests/data/janis/wgs_somatic_dep/__init__.py' 2023-09-27T07:49:56,793 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wgssomatic.py' 2023-09-27T07:49:56,794 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wgssomatic_variantsonly.py' 2023-09-27T07:49:56,796 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/WGSSomaticMultiCallers-inp.yml' 2023-09-27T07:49:56,798 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/WGSSomaticMultiCallers_1_4_0.cwl' 2023-09-27T07:49:56,800 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/AddBamStatsSomatic_v0_1_0.cwl' 2023-09-27T07:49:56,802 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/BwaAligner_1_0_0.cwl' 2023-09-27T07:49:56,803 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/BwaMemSamtoolsView_0_7_17_1_9.cwl' 2023-09-27T07:49:56,805 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/ConcatStrelkaSomaticVcf_0_1_16.cwl' 2023-09-27T07:49:56,806 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/FilterVardictSomaticVcf_v1_9.cwl' 2023-09-27T07:49:56,807 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/GATK4_SomaticVariantCaller_4_1_3_0.cwl' 2023-09-27T07:49:56,809 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/GATKBaseRecalBQSRWorkflow_4_1_3.cwl' 2023-09-27T07:49:56,810 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4ApplyBQSR_4_1_3_0.cwl' 2023-09-27T07:49:56,812 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4BaseRecalibrator_4_1_3_0.cwl' 2023-09-27T07:49:56,813 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4CalculateContamination_4_1_4_0.cwl' 2023-09-27T07:49:56,815 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4CollectInsertSizeMetrics_4_1_3_0.cwl' 2023-09-27T07:49:56,816 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4FilterMutectCalls_4_1_3_0.cwl' 2023-09-27T07:49:56,817 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4GatherVcfs_4_1_3_0.cwl' 2023-09-27T07:49:56,819 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4GetPileupSummaries_4_1_6_0.cwl' 2023-09-27T07:49:56,820 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4LearnReadOrientationModel_4_1_4_0.cwl' 2023-09-27T07:49:56,822 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4MarkDuplicates_4_1_3_0.cwl' 2023-09-27T07:49:56,824 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4MergeSamFiles_4_1_3_0.cwl' 2023-09-27T07:49:56,828 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4Mutect2_4_1_3_0.cwl' 2023-09-27T07:49:56,830 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4SortSam_4_1_2_0.cwl' 2023-09-27T07:49:56,832 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/Gatk4SplitReads_4_1_3_0.cwl' 2023-09-27T07:49:56,834 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/GenerateGenomeFileForBedtoolsCoverage_v0_1_0.cwl' 2023-09-27T07:49:56,836 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/GenerateVardictHeaderLines_v0_1_0.cwl' 2023-09-27T07:49:56,837 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/ParseFastqcAdaptors_v0_1_0.cwl' 2023-09-27T07:49:56,839 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/PerformanceSummaryGenome_v0_1_0.cwl' 2023-09-27T07:49:56,840 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/SamToolsFlagstat_1_9_0.cwl' 2023-09-27T07:49:56,841 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/SamToolsMpileup_1_9_0.cwl' 2023-09-27T07:49:56,843 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/SamToolsView_1_9_0.cwl' 2023-09-27T07:49:56,844 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/SplitMultiAllele_v0_5772.cwl' 2023-09-27T07:49:56,845 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/UncompressArchive_v1_0_0.cwl' 2023-09-27T07:49:56,846 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/VcfTools_0_1_16.cwl' 2023-09-27T07:49:56,848 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/addBamStats_0_0_7.cwl' 2023-09-27T07:49:56,849 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/bcftoolsAnnotate_v1_5.cwl' 2023-09-27T07:49:56,850 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/bcftoolssort_v1_9.cwl' 2023-09-27T07:49:56,852 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/bedtoolsgenomeCoverageBed_v2_29_2.cwl' 2023-09-27T07:49:56,853 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/bgzip_1_2_1.cwl' 2023-09-27T07:49:56,855 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/combinevariants_0_0_8.cwl' 2023-09-27T07:49:56,857 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/cutadapt_2_1.cwl' 2023-09-27T07:49:56,858 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/extractStrelkaSomaticADDP_0_1_1.cwl' 2023-09-27T07:49:56,859 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/fastqc_v0_11_8.cwl' 2023-09-27T07:49:56,861 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/gridss_v2_6_2.cwl' 2023-09-27T07:49:56,862 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/manta_1_5_0.cwl' 2023-09-27T07:49:56,864 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/mergeAndMarkBams_4_1_3.cwl' 2023-09-27T07:49:56,865 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/performanceSummary_0_0_7.cwl' 2023-09-27T07:49:56,866 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/samtools_mpileup_subpipeline.cwl' 2023-09-27T07:49:56,868 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/somatic_subpipeline.cwl' 2023-09-27T07:49:56,869 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/split_bam_subpipeline.cwl' 2023-09-27T07:49:56,870 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/strelkaSomaticVariantCaller_v0_1_1.cwl' 2023-09-27T07:49:56,872 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/strelka_somatic_2_9_10.cwl' 2023-09-27T07:49:56,873 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/tabix_1_2_1.cwl' 2023-09-27T07:49:56,875 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/trimIUPAC_0_0_5.cwl' 2023-09-27T07:49:56,876 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/vardictSomaticVariantCaller_v0_1_0.cwl' 2023-09-27T07:49:56,878 adding 'janis_core/tests/data/janis/wgs_somatic_dep/cwl/tools/vardict_somatic_1_6_0.cwl' 2023-09-27T07:49:56,880 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/WGSSomaticMultiCallers-inp.json' 2023-09-27T07:49:56,881 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/WGSSomaticMultiCallers_1_4_0.wdl' 2023-09-27T07:49:56,884 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/AddBamStatsSomatic_v0_1_0.wdl' 2023-09-27T07:49:56,885 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/BwaAligner_1_0_0.wdl' 2023-09-27T07:49:56,886 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/BwaMemSamtoolsView_0_7_17_1_9.wdl' 2023-09-27T07:49:56,888 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/ConcatStrelkaSomaticVcf_0_1_16.wdl' 2023-09-27T07:49:56,889 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/FilterVardictSomaticVcf_v1_9.wdl' 2023-09-27T07:49:56,890 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/GATK4_SomaticVariantCaller_4_1_3_0.wdl' 2023-09-27T07:49:56,891 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/GATKBaseRecalBQSRWorkflow_4_1_3.wdl' 2023-09-27T07:49:56,893 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4ApplyBQSR_4_1_3_0.wdl' 2023-09-27T07:49:56,894 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4BaseRecalibrator_4_1_3_0.wdl' 2023-09-27T07:49:56,895 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4CalculateContamination_4_1_4_0.wdl' 2023-09-27T07:49:56,896 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4CollectInsertSizeMetrics_4_1_3_0.wdl' 2023-09-27T07:49:56,897 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4FilterMutectCalls_4_1_3_0.wdl' 2023-09-27T07:49:56,899 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4GatherVcfs_4_1_3_0.wdl' 2023-09-27T07:49:56,900 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4GetPileupSummaries_4_1_6_0.wdl' 2023-09-27T07:49:56,901 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4LearnReadOrientationModel_4_1_4_0.wdl' 2023-09-27T07:49:56,903 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4MarkDuplicates_4_1_3_0.wdl' 2023-09-27T07:49:56,904 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4MergeSamFiles_4_1_3_0.wdl' 2023-09-27T07:49:56,906 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4Mutect2_4_1_3_0.wdl' 2023-09-27T07:49:56,908 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4SortSam_4_1_2_0.wdl' 2023-09-27T07:49:56,910 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/Gatk4SplitReads_4_1_3_0.wdl' 2023-09-27T07:49:56,911 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/GenerateGenomeFileForBedtoolsCoverage_v0_1_0.wdl' 2023-09-27T07:49:56,912 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/GenerateVardictHeaderLines_v0_1_0.wdl' 2023-09-27T07:49:56,914 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/ParseFastqcAdaptors_v0_1_0.wdl' 2023-09-27T07:49:56,915 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/PerformanceSummaryGenome_v0_1_0.wdl' 2023-09-27T07:49:56,916 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/SamToolsFlagstat_1_9_0.wdl' 2023-09-27T07:49:56,918 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/SamToolsMpileup_1_9_0.wdl' 2023-09-27T07:49:56,919 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/SamToolsView_1_9_0.wdl' 2023-09-27T07:49:56,920 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/SplitMultiAllele_v0_5772.wdl' 2023-09-27T07:49:56,921 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/UncompressArchive_v1_0_0.wdl' 2023-09-27T07:49:56,923 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/VcfTools_0_1_16.wdl' 2023-09-27T07:49:56,924 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/addBamStats_0_0_7.wdl' 2023-09-27T07:49:56,926 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/bcftoolsAnnotate_v1_5.wdl' 2023-09-27T07:49:56,927 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/bcftoolssort_v1_9.wdl' 2023-09-27T07:49:56,928 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/bedtoolsgenomeCoverageBed_v2_29_2.wdl' 2023-09-27T07:49:56,930 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/bgzip_1_2_1.wdl' 2023-09-27T07:49:56,931 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/combinevariants_0_0_8.wdl' 2023-09-27T07:49:56,932 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/cutadapt_2_1.wdl' 2023-09-27T07:49:56,934 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/extractStrelkaSomaticADDP_0_1_1.wdl' 2023-09-27T07:49:56,935 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/fastqc_v0_11_8.wdl' 2023-09-27T07:49:56,936 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/gridss_v2_6_2.wdl' 2023-09-27T07:49:56,937 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/manta_1_5_0.wdl' 2023-09-27T07:49:56,939 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/mergeAndMarkBams_4_1_3.wdl' 2023-09-27T07:49:56,940 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/performanceSummary_0_0_7.wdl' 2023-09-27T07:49:56,941 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/samtools_mpileup_subpipeline.wdl' 2023-09-27T07:49:56,942 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/somatic_subpipeline.wdl' 2023-09-27T07:49:56,943 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/split_bam_subpipeline.wdl' 2023-09-27T07:49:56,945 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/strelkaSomaticVariantCaller_v0_1_1.wdl' 2023-09-27T07:49:56,946 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/strelka_somatic_2_9_10.wdl' 2023-09-27T07:49:56,947 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/tabix_1_2_1.wdl' 2023-09-27T07:49:56,949 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/trimIUPAC_0_0_5.wdl' 2023-09-27T07:49:56,950 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/vardictSomaticVariantCaller_v0_1_0.wdl' 2023-09-27T07:49:56,951 adding 'janis_core/tests/data/janis/wgs_somatic_dep/wdl/tools/vardict_somatic_1_6_0.wdl' 2023-09-27T07:49:56,955 adding 'janis_core/tests/data/wdl/Multisample_jointgt_GATK4.wdl' 2023-09-27T07:49:56,957 adding 'janis_core/tests/data/wdl/bwa.wdl' 2023-09-27T07:49:56,959 adding 'janis_core/tests/data/wdl/somatic_wf.wdl' 2023-09-27T07:49:56,961 adding 'janis_core/tests/integration/README.md' 2023-09-27T07:49:56,962 adding 'janis_core/tests/integration/__init__.py' 2023-09-27T07:49:56,963 adding 'janis_core/tests/integration/test_directorygenerator.py' 2023-09-27T07:49:56,965 adding 'janis_core/tests/mock/__init__.py' 2023-09-27T07:49:56,966 adding 'janis_core/tests/mock/mock_components.py' 2023-09-27T07:49:56,968 adding 'janis_core/tests/mock/mock_entities.py' 2023-09-27T07:49:56,969 adding 'janis_core/tests/mock/mock_metadata.py' 2023-09-27T07:49:56,970 adding 'janis_core/tests/mock/mock_params.py' 2023-09-27T07:49:56,971 adding 'janis_core/tests/mock/mock_tool.py' 2023-09-27T07:49:56,972 adding 'janis_core/tests/mock/mock_workflow.py' 2023-09-27T07:49:56,974 adding 'janis_core/tests/mock/mock_xmltool.py' 2023-09-27T07:49:56,975 adding 'janis_core/tests/mock/cwl/__init__.py' 2023-09-27T07:49:56,976 adding 'janis_core/tests/mock/cwl/tools.py' 2023-09-27T07:49:56,978 adding 'janis_core/tests/mock/cwl/workflows.py' 2023-09-27T07:49:56,979 adding 'janis_core/tests/testtools/__init__.py' 2023-09-27T07:49:56,981 adding 'janis_core/tests/testtools/arrays.py' 2023-09-27T07:49:56,982 adding 'janis_core/tests/testtools/basics.py' 2023-09-27T07:49:56,984 adding 'janis_core/tests/testtools/bwamem.py' 2023-09-27T07:49:56,985 adding 'janis_core/tests/testtools/components.py' 2023-09-27T07:49:56,987 adding 'janis_core/tests/testtools/fastqc.py' 2023-09-27T07:49:56,989 adding 'janis_core/tests/testtools/gridss.py' 2023-09-27T07:49:56,990 adding 'janis_core/tests/testtools/misc_codetools.py' 2023-09-27T07:49:56,991 adding 'janis_core/tests/testtools/misc_commandtools.py' 2023-09-27T07:49:56,993 adding 'janis_core/tests/testtools/types.py' 2023-09-27T07:49:56,995 adding 'janis_core/tests/testtools/unicycler.py' 2023-09-27T07:49:56,997 adding 'janis_core/tests/testworkflows/__init__.py' 2023-09-27T07:49:56,999 adding 'janis_core/tests/testworkflows/additional_features.py' 2023-09-27T07:49:57,000 adding 'janis_core/tests/testworkflows/all_input_types.py' 2023-09-27T07:49:57,002 adding 'janis_core/tests/testworkflows/assembly.py' 2023-09-27T07:49:57,003 adding 'janis_core/tests/testworkflows/basics.py' 2023-09-27T07:49:57,005 adding 'janis_core/tests/testworkflows/call.py' 2023-09-27T07:49:57,006 adding 'janis_core/tests/testworkflows/codetools.py' 2023-09-27T07:49:57,008 adding 'janis_core/tests/testworkflows/combos.py' 2023-09-27T07:49:57,009 adding 'janis_core/tests/testworkflows/components.py' 2023-09-27T07:49:57,010 adding 'janis_core/tests/testworkflows/data_sources.py' 2023-09-27T07:49:57,011 adding 'janis_core/tests/testworkflows/duplicate_tasks.py' 2023-09-27T07:49:57,013 adding 'janis_core/tests/testworkflows/file_pairs.py' 2023-09-27T07:49:57,014 adding 'janis_core/tests/testworkflows/filenames.py' 2023-09-27T07:49:57,015 adding 'janis_core/tests/testworkflows/files_directories_to_create.py' 2023-09-27T07:49:57,017 adding 'janis_core/tests/testworkflows/mandatory_types.py' 2023-09-27T07:49:57,018 adding 'janis_core/tests/testworkflows/minimal_task_inputs.py' 2023-09-27T07:49:57,019 adding 'janis_core/tests/testworkflows/naming.py' 2023-09-27T07:49:57,021 adding 'janis_core/tests/testworkflows/operations.py' 2023-09-27T07:49:57,022 adding 'janis_core/tests/testworkflows/optional_types.py' 2023-09-27T07:49:57,023 adding 'janis_core/tests/testworkflows/ordering.py' 2023-09-27T07:49:57,025 adding 'janis_core/tests/testworkflows/outputs.py' 2023-09-27T07:49:57,026 adding 'janis_core/tests/testworkflows/plumbing_edge_cases.py' 2023-09-27T07:49:57,027 adding 'janis_core/tests/testworkflows/plumbing_scatter.py' 2023-09-27T07:49:57,028 adding 'janis_core/tests/testworkflows/plumbing_type_mismatch.py' 2023-09-27T07:49:57,029 adding 'janis_core/tests/testworkflows/preprocessing_prune.py' 2023-09-27T07:49:57,031 adding 'janis_core/tests/testworkflows/process_inputs.py' 2023-09-27T07:49:57,032 adding 'janis_core/tests/testworkflows/scatter.py' 2023-09-27T07:49:57,033 adding 'janis_core/tests/testworkflows/script.py' 2023-09-27T07:49:57,036 adding 'janis_core/tests/testworkflows/secondaries.py' 2023-09-27T07:49:57,038 adding 'janis_core/tests/testworkflows/string_formatter.py' 2023-09-27T07:49:57,039 adding 'janis_core/tests/testworkflows/subworkflow.py' 2023-09-27T07:49:57,040 adding 'janis_core/tests/testworkflows/subworkflow2.py' 2023-09-27T07:49:57,042 adding 'janis_core/tests/testworkflows/trace.py' 2023-09-27T07:49:57,043 adding 'janis_core/tests/testworkflows/unwrap.py' 2023-09-27T07:49:57,045 adding 'janis_core/tool/__init__.py' 2023-09-27T07:49:57,046 adding 'janis_core/tool/batchrun.py' 2023-09-27T07:49:57,050 adding 'janis_core/tool/commandtool.py' 2023-09-27T07:49:57,051 adding 'janis_core/tool/cwl_tool_parser.py' 2023-09-27T07:49:57,053 adding 'janis_core/tool/documentation.py' 2023-09-27T07:49:57,054 adding 'janis_core/tool/test_classes.py' 2023-09-27T07:49:57,056 adding 'janis_core/tool/test_definitions.py' 2023-09-27T07:49:57,057 adding 'janis_core/tool/test_helpers.py' 2023-09-27T07:49:57,060 adding 'janis_core/tool/test_suite_runner.py' 2023-09-27T07:49:57,062 adding 'janis_core/tool/tool.py' 2023-09-27T07:49:57,063 adding 'janis_core/toolbox/__init__.py' 2023-09-27T07:49:57,065 adding 'janis_core/toolbox/entrypoints.py' 2023-09-27T07:49:57,066 adding 'janis_core/toolbox/register.py' 2023-09-27T07:49:57,068 adding 'janis_core/toolbox/toolbox.py' 2023-09-27T07:49:57,070 adding 'janis_core/transformation/__init__.py' 2023-09-27T07:49:57,072 adding 'janis_core/translation_deps/__init__.py' 2023-09-27T07:49:57,073 adding 'janis_core/translation_deps/exportpath.py' 2023-09-27T07:49:57,075 adding 'janis_core/translation_deps/supportedtranslations.py' 2023-09-27T07:49:57,076 adding 'janis_core/translation_utils/__init__.py' 2023-09-27T07:49:57,078 adding 'janis_core/translation_utils/datatypes.py' 2023-09-27T07:49:57,079 adding 'janis_core/translation_utils/graph.py' 2023-09-27T07:49:57,081 adding 'janis_core/translations/__init__.py' 2023-09-27T07:49:57,083 adding 'janis_core/translations/main.py' 2023-09-27T07:49:57,085 adding 'janis_core/translations/translationbase.py' 2023-09-27T07:49:57,087 adding 'janis_core/translations/common/__init__.py' 2023-09-27T07:49:57,089 adding 'janis_core/translations/common/trace.py' 2023-09-27T07:49:57,090 adding 'janis_core/translations/common/preprocessing/__init__.py' 2023-09-27T07:49:57,092 adding 'janis_core/translations/common/preprocessing/builders/__init__.py' 2023-09-27T07:49:57,093 adding 'janis_core/translations/common/preprocessing/builders/main.py' 2023-09-27T07:49:57,094 adding 'janis_core/translations/common/preprocessing/prune/__init__.py' 2023-09-27T07:49:57,096 adding 'janis_core/translations/common/preprocessing/prune/common.py' 2023-09-27T07:49:57,097 adding 'janis_core/translations/common/preprocessing/prune/gather.py' 2023-09-27T07:49:57,098 adding 'janis_core/translations/common/preprocessing/prune/history.py' 2023-09-27T07:49:57,099 adding 'janis_core/translations/common/preprocessing/prune/main.py' 2023-09-27T07:49:57,101 adding 'janis_core/translations/common/preprocessing/prune/tools.py' 2023-09-27T07:49:57,102 adding 'janis_core/translations/common/preprocessing/prune/workflows.py' 2023-09-27T07:49:57,104 adding 'janis_core/translations/cwl/__init__.py' 2023-09-27T07:49:57,111 adding 'janis_core/translations/cwl/main.py' 2023-09-27T07:49:57,113 adding 'janis_core/translations/janis/__init__.py' 2023-09-27T07:49:57,116 adding 'janis_core/translations/janis/main.py' 2023-09-27T07:49:57,118 adding 'janis_core/translations/nextflow/__init__.py' 2023-09-27T07:49:57,119 adding 'janis_core/translations/nextflow/expressions.py' 2023-09-27T07:49:57,121 adding 'janis_core/translations/nextflow/main.py' 2023-09-27T07:49:57,122 adding 'janis_core/translations/nextflow/nfgen_utils.py' 2023-09-27T07:49:57,124 adding 'janis_core/translations/nextflow/nulls.py' 2023-09-27T07:49:57,125 adding 'janis_core/translations/nextflow/scope.py' 2023-09-27T07:49:57,126 adding 'janis_core/translations/nextflow/task_inputs.py' 2023-09-27T07:49:57,130 adding 'janis_core/translations/nextflow/unwrap.py' 2023-09-27T07:49:57,132 adding 'janis_core/translations/nextflow/variables.py' 2023-09-27T07:49:57,134 adding 'janis_core/translations/nextflow/casefmt/__init__.py' 2023-09-27T07:49:57,135 adding 'janis_core/translations/nextflow/casefmt/casefmt.py' 2023-09-27T07:49:57,136 adding 'janis_core/translations/nextflow/casefmt/mapping.py' 2023-09-27T07:49:57,137 adding 'janis_core/translations/nextflow/casefmt/patterns.py' 2023-09-27T07:49:57,139 adding 'janis_core/translations/nextflow/generate/__init__.py' 2023-09-27T07:49:57,140 adding 'janis_core/translations/nextflow/generate/config.py' 2023-09-27T07:49:57,142 adding 'janis_core/translations/nextflow/generate/files/__init__.py' 2023-09-27T07:49:57,144 adding 'janis_core/translations/nextflow/generate/files/channel_declarations.py' 2023-09-27T07:49:57,145 adding 'janis_core/translations/nextflow/generate/files/main.py' 2023-09-27T07:49:57,147 adding 'janis_core/translations/nextflow/generate/files/process.py' 2023-09-27T07:49:57,148 adding 'janis_core/translations/nextflow/generate/files/variable_declarations.py' 2023-09-27T07:49:57,150 adding 'janis_core/translations/nextflow/generate/files/workflow.py' 2023-09-27T07:49:57,151 adding 'janis_core/translations/nextflow/generate/process/__init__.py' 2023-09-27T07:49:57,153 adding 'janis_core/translations/nextflow/generate/process/directives.py' 2023-09-27T07:49:57,155 adding 'janis_core/translations/nextflow/generate/process/inputs.py' 2023-09-27T07:49:57,156 adding 'janis_core/translations/nextflow/generate/process/main.py' 2023-09-27T07:49:57,158 adding 'janis_core/translations/nextflow/generate/process/outputs/__init__.py' 2023-09-27T07:49:57,160 adding 'janis_core/translations/nextflow/generate/process/outputs/factory_cmdtool.py' 2023-09-27T07:49:57,161 adding 'janis_core/translations/nextflow/generate/process/outputs/factory_pythontool.py' 2023-09-27T07:49:57,163 adding 'janis_core/translations/nextflow/generate/process/outputs/main.py' 2023-09-27T07:49:57,165 adding 'janis_core/translations/nextflow/generate/process/script/__init__.py' 2023-09-27T07:49:57,166 adding 'janis_core/translations/nextflow/generate/process/script/attributes.py' 2023-09-27T07:49:57,167 adding 'janis_core/translations/nextflow/generate/process/script/common.py' 2023-09-27T07:49:57,168 adding 'janis_core/translations/nextflow/generate/process/script/ctype.py' 2023-09-27T07:49:57,170 adding 'janis_core/translations/nextflow/generate/process/script/main.py' 2023-09-27T07:49:57,171 adding 'janis_core/translations/nextflow/generate/process/script/ordering.py' 2023-09-27T07:49:57,173 adding 'janis_core/translations/nextflow/generate/process/script/prescript.py' 2023-09-27T07:49:57,175 adding 'janis_core/translations/nextflow/generate/process/script/script.py' 2023-09-27T07:49:57,176 adding 'janis_core/translations/nextflow/generate/process/script/selection.py' 2023-09-27T07:49:57,178 adding 'janis_core/translations/nextflow/generate/workflow/__init__.py' 2023-09-27T07:49:57,180 adding 'janis_core/translations/nextflow/generate/workflow/call.py' 2023-09-27T07:49:57,181 adding 'janis_core/translations/nextflow/generate/workflow/common.py' 2023-09-27T07:49:57,183 adding 'janis_core/translations/nextflow/generate/workflow/datatype_mismatch.py' 2023-09-27T07:49:57,184 adding 'janis_core/translations/nextflow/generate/workflow/edge_cases.py' 2023-09-27T07:49:57,186 adding 'janis_core/translations/nextflow/generate/workflow/main.py' 2023-09-27T07:49:57,187 adding 'janis_core/translations/nextflow/generate/workflow/scatter.py' 2023-09-27T07:49:57,189 adding 'janis_core/translations/nextflow/model/__init__.py' 2023-09-27T07:49:57,190 adding 'janis_core/translations/nextflow/model/files/__init__.py' 2023-09-27T07:49:57,192 adding 'janis_core/translations/nextflow/model/files/channels.py' 2023-09-27T07:49:57,193 adding 'janis_core/translations/nextflow/model/files/files.py' 2023-09-27T07:49:57,194 adding 'janis_core/translations/nextflow/model/files/variables.py' 2023-09-27T07:49:57,196 adding 'janis_core/translations/nextflow/model/process/__init__.py' 2023-09-27T07:49:57,198 adding 'janis_core/translations/nextflow/model/process/directives.py' 2023-09-27T07:49:57,199 adding 'janis_core/translations/nextflow/model/process/inputs.py' 2023-09-27T07:49:57,200 adding 'janis_core/translations/nextflow/model/process/outputs.py' 2023-09-27T07:49:57,202 adding 'janis_core/translations/nextflow/model/process/process.py' 2023-09-27T07:49:57,204 adding 'janis_core/translations/nextflow/model/workflow/__init__.py' 2023-09-27T07:49:57,205 adding 'janis_core/translations/nextflow/model/workflow/workflow.py' 2023-09-27T07:49:57,207 adding 'janis_core/translations/nextflow/naming/__init__.py' 2023-09-27T07:49:57,208 adding 'janis_core/translations/nextflow/naming/constructs.py' 2023-09-27T07:49:57,209 adding 'janis_core/translations/nextflow/naming/process.py' 2023-09-27T07:49:57,211 adding 'janis_core/translations/nextflow/params/__init__.py' 2023-09-27T07:49:57,213 adding 'janis_core/translations/nextflow/params/main.py' 2023-09-27T07:49:57,214 adding 'janis_core/translations/nextflow/params/update.py' 2023-09-27T07:49:57,216 adding 'janis_core/translations/nextflow/preprocessing/__init__.py' 2023-09-27T07:49:57,217 adding 'janis_core/translations/nextflow/preprocessing/unique_task_names.py' 2023-09-27T07:49:57,219 adding 'janis_core/translations/nextflow/preprocessing/task_inputs/__init__.py' 2023-09-27T07:49:57,220 adding 'janis_core/translations/nextflow/preprocessing/task_inputs/categories.py' 2023-09-27T07:49:57,222 adding 'janis_core/translations/nextflow/preprocessing/task_inputs/common.py' 2023-09-27T07:49:57,223 adding 'janis_core/translations/nextflow/preprocessing/task_inputs/history.py' 2023-09-27T07:49:57,225 adding 'janis_core/translations/nextflow/preprocessing/task_inputs/main.py' 2023-09-27T07:49:57,227 adding 'janis_core/translations/nextflow/preprocessing/task_inputs/populator.py' 2023-09-27T07:49:57,228 adding 'janis_core/translations/wdl/__init__.py' 2023-09-27T07:49:57,238 adding 'janis_core/translations/wdl/main.py' 2023-09-27T07:49:57,240 adding 'janis_core/translations/wdl/ordering.py' 2023-09-27T07:49:57,241 adding 'janis_core/types/__init__.py' 2023-09-27T07:49:57,245 adding 'janis_core/types/common_data_types.py' 2023-09-27T07:49:57,247 adding 'janis_core/types/data_types.py' 2023-09-27T07:49:57,249 adding 'janis_core/utils/__init__.py' 2023-09-27T07:49:57,250 adding 'janis_core/utils/bracketmatching.py' 2023-09-27T07:49:57,251 adding 'janis_core/utils/docparser_info.py' 2023-09-27T07:49:57,253 adding 'janis_core/utils/errors.py' 2023-09-27T07:49:57,254 adding 'janis_core/utils/generators.py' 2023-09-27T07:49:57,255 adding 'janis_core/utils/generics_util.py' 2023-09-27T07:49:57,256 adding 'janis_core/utils/janisconstants.py' 2023-09-27T07:49:57,257 adding 'janis_core/utils/levenshteindistance.py' 2023-09-27T07:49:57,259 adding 'janis_core/utils/logger.py' 2023-09-27T07:49:57,260 adding 'janis_core/utils/metadata.py' 2023-09-27T07:49:57,261 adding 'janis_core/utils/pickvalue.py' 2023-09-27T07:49:57,263 adding 'janis_core/utils/scatter.py' 2023-09-27T07:49:57,264 adding 'janis_core/utils/secondary.py' 2023-09-27T07:49:57,265 adding 'janis_core/utils/validators.py' 2023-09-27T07:49:57,266 adding 'janis_core/utils/yaml_utils.py' 2023-09-27T07:49:57,268 adding 'janis_core/workflow/__init__.py' 2023-09-27T07:49:57,274 adding 'janis_core/workflow/workflow.py' 2023-09-27T07:49:57,281 adding 'janis_pipelines.core-0.13.1.dist-info/LICENSE' 2023-09-27T07:49:57,288 adding 'janis_pipelines.core-0.13.1.dist-info/METADATA' 2023-09-27T07:49:57,289 adding 'janis_pipelines.core-0.13.1.dist-info/WHEEL' 2023-09-27T07:49:57,290 adding 'janis_pipelines.core-0.13.1.dist-info/top_level.txt' 2023-09-27T07:49:57,333 adding 'janis_pipelines.core-0.13.1.dist-info/RECORD' 2023-09-27T07:49:57,368 removing build/bdist.linux-armv7l/wheel 2023-09-27T07:49:58,145 Building wheel for janis-pipelines-core (pyproject.toml): finished with status 'done' 2023-09-27T07:49:59,845 Created wheel for janis-pipelines-core: filename=janis_pipelines.core-0.13.1-py3-none-any.whl size=75015026 sha256=71ee00cd429ff1a731b5ebc5ae6ae76eae2b1940dd3866477453af413aeed8e2 2023-09-27T07:49:59,847 Stored in directory: /tmp/pip-ephem-wheel-cache-n8nvjg3b/wheels/37/2a/3e/3b6f5725871d3fabfed21ea11af4789c584cd297a15d65a386 2023-09-27T07:49:59,965 Successfully built janis-pipelines-core 2023-09-27T07:50:01,873 Removed build tracker: '/tmp/pip-build-tracker-p669mipu'