.gitignore
.pre-commit-config.yaml
LICENSE
README.md
constants.py
notes.txt
pyproject.toml
setup.py
.github/workflows/publish.yml
.github/workflows/unit_tests.yml
janis_core/__init__.py
janis_core/__meta__.py
janis_core/code/__init__.py
janis_core/code/codetool.py
janis_core/code/pythontool.py
janis_core/graph/__init__.py
janis_core/graph/node.py
janis_core/graph/steptaginput.py
janis_core/hints/__init__.py
janis_core/ingestion/SupportedIngestion.py
janis_core/ingestion/__init__.py
janis_core/ingestion/main.py
janis_core/ingestion/cwl/__init__.py
janis_core/ingestion/cwl/expressions.py
janis_core/ingestion/cwl/graph.py
janis_core/ingestion/cwl/identifiers.py
janis_core/ingestion/cwl/loading.py
janis_core/ingestion/cwl/main.py
janis_core/ingestion/cwl/preprocessing.py
janis_core/ingestion/cwl/types.py
janis_core/ingestion/cwl/parsing/__init__.py
janis_core/ingestion/cwl/parsing/tool.py
janis_core/ingestion/cwl/parsing/workflow.py
janis_core/ingestion/data/janis_types.yaml
janis_core/ingestion/data/logging_config.yaml
janis_core/ingestion/data/galaxy/datatypes_conf.xml.sample
janis_core/ingestion/data/galaxy/galaxy_config.yaml
janis_core/ingestion/galaxy/__init__.py
janis_core/ingestion/galaxy/aliases.py
janis_core/ingestion/galaxy/ingest.py
janis_core/ingestion/galaxy/logging.py
janis_core/ingestion/galaxy/containers/Container.py
janis_core/ingestion/galaxy/containers/__init__.py
janis_core/ingestion/galaxy/containers/cache.py
janis_core/ingestion/galaxy/containers/fetch.py
janis_core/ingestion/galaxy/containers/main.py
janis_core/ingestion/galaxy/containers/mulled.py
janis_core/ingestion/galaxy/containers/fetching/ContainerReqFetcher.py
janis_core/ingestion/galaxy/containers/fetching/Fetcher.py
janis_core/ingestion/galaxy/containers/fetching/GA4GHFetcher.py
janis_core/ingestion/galaxy/containers/fetching/QuayIOFetcher.py
janis_core/ingestion/galaxy/containers/fetching/__init__.py
janis_core/ingestion/galaxy/containers/fetching/presets.py
janis_core/ingestion/galaxy/containers/fetching/utils.py
janis_core/ingestion/galaxy/containers/selection/VersionMatcher.py
janis_core/ingestion/galaxy/containers/selection/__init__.py
janis_core/ingestion/galaxy/containers/selection/selection.py
janis_core/ingestion/galaxy/datatypes/JanisDatatype.py
janis_core/ingestion/galaxy/datatypes/__init__.py
janis_core/ingestion/galaxy/datatypes/conversion.py
janis_core/ingestion/galaxy/datatypes/core.py
janis_core/ingestion/galaxy/datatypes/galaxy.py
janis_core/ingestion/galaxy/datatypes/main.py
janis_core/ingestion/galaxy/datatypes/register.py
janis_core/ingestion/galaxy/datatypes/strategies.py
janis_core/ingestion/galaxy/expressions/__init__.py
janis_core/ingestion/galaxy/expressions/checks.py
janis_core/ingestion/galaxy/expressions/matches.py
janis_core/ingestion/galaxy/expressions/patterns.py
janis_core/ingestion/galaxy/fileio/__init__.py
janis_core/ingestion/galaxy/fileio/initialisation.py
janis_core/ingestion/galaxy/fileio/write.py
janis_core/ingestion/galaxy/fileio/formats/DefaultFormat.py
janis_core/ingestion/galaxy/fileio/formats/Format.py
janis_core/ingestion/galaxy/fileio/formats/SubworkflowFormat.py
janis_core/ingestion/galaxy/fileio/formats/__init__.py
janis_core/ingestion/galaxy/fileio/text/TextRender.py
janis_core/ingestion/galaxy/fileio/text/__init__.py
janis_core/ingestion/galaxy/fileio/text/formatting.py
janis_core/ingestion/galaxy/fileio/text/ordering.py
janis_core/ingestion/galaxy/fileio/text/tool/ConfigfileText.py
janis_core/ingestion/galaxy/fileio/text/tool/ToolInputSectionText.py
janis_core/ingestion/galaxy/fileio/text/tool/ToolInputText.py
janis_core/ingestion/galaxy/fileio/text/tool/ToolOutputSectionText.py
janis_core/ingestion/galaxy/fileio/text/tool/ToolOutputText.py
janis_core/ingestion/galaxy/fileio/text/tool/ToolText.py
janis_core/ingestion/galaxy/fileio/text/tool/UnstranslatedText.py
janis_core/ingestion/galaxy/fileio/text/tool/__init__.py
janis_core/ingestion/galaxy/fileio/text/workflow/ConfigText.py
janis_core/ingestion/galaxy/fileio/text/workflow/InputsText.py
janis_core/ingestion/galaxy/fileio/text/workflow/StepText.py
janis_core/ingestion/galaxy/fileio/text/workflow/WorkflowInputText.py
janis_core/ingestion/galaxy/fileio/text/workflow/WorkflowOutputText.py
janis_core/ingestion/galaxy/fileio/text/workflow/WorkflowText.py
janis_core/ingestion/galaxy/fileio/text/workflow/__init__.py
janis_core/ingestion/galaxy/gxtool/TestRegister.py
janis_core/ingestion/galaxy/gxtool/__init__.py
janis_core/ingestion/galaxy/gxtool/mock.py
janis_core/ingestion/galaxy/gxtool/command/Command.py
janis_core/ingestion/galaxy/gxtool/command/__init__.py
janis_core/ingestion/galaxy/gxtool/command/annotation.py
janis_core/ingestion/galaxy/gxtool/command/epaths.py
janis_core/ingestion/galaxy/gxtool/command/loading.py
janis_core/ingestion/galaxy/gxtool/command/main.py
janis_core/ingestion/galaxy/gxtool/command/tokenise.py
janis_core/ingestion/galaxy/gxtool/command/update.py
janis_core/ingestion/galaxy/gxtool/command/cmdstr/CommandString.py
janis_core/ingestion/galaxy/gxtool/command/cmdstr/DynamicCommandStatement.py
janis_core/ingestion/galaxy/gxtool/command/cmdstr/MainStatementInferrer.py
janis_core/ingestion/galaxy/gxtool/command/cmdstr/RealisedTokenValues.py
janis_core/ingestion/galaxy/gxtool/command/cmdstr/__init__.py
janis_core/ingestion/galaxy/gxtool/command/cmdstr/analysis.py
janis_core/ingestion/galaxy/gxtool/command/cmdstr/constructs.py
janis_core/ingestion/galaxy/gxtool/command/cmdstr/generate.py
janis_core/ingestion/galaxy/gxtool/command/cmdstr/utils.py
janis_core/ingestion/galaxy/gxtool/command/components/CommandComponent.py
janis_core/ingestion/galaxy/gxtool/command/components/ValueRecord.py
janis_core/ingestion/galaxy/gxtool/command/components/__init__.py
janis_core/ingestion/galaxy/gxtool/command/components/factory.py
janis_core/ingestion/galaxy/gxtool/command/components/inputs/Flag.py
janis_core/ingestion/galaxy/gxtool/command/components/inputs/InputComponent.py
janis_core/ingestion/galaxy/gxtool/command/components/inputs/Option.py
janis_core/ingestion/galaxy/gxtool/command/components/inputs/Positional.py
janis_core/ingestion/galaxy/gxtool/command/components/inputs/__init__.py
janis_core/ingestion/galaxy/gxtool/command/components/inputs/utils.py
janis_core/ingestion/galaxy/gxtool/command/components/linux/Tee.py
janis_core/ingestion/galaxy/gxtool/command/components/linux/__init__.py
janis_core/ingestion/galaxy/gxtool/command/components/linux/streams.py
janis_core/ingestion/galaxy/gxtool/command/components/outputs/InputOutput.py
janis_core/ingestion/galaxy/gxtool/command/components/outputs/OutputComponent.py
janis_core/ingestion/galaxy/gxtool/command/components/outputs/RedirectOutput.py
janis_core/ingestion/galaxy/gxtool/command/components/outputs/WildcardOutput.py
janis_core/ingestion/galaxy/gxtool/command/components/outputs/__init__.py
janis_core/ingestion/galaxy/gxtool/command/epath/Annotator.py
janis_core/ingestion/galaxy/gxtool/command/epath/ComponentOrderingStrategy.py
janis_core/ingestion/galaxy/gxtool/command/epath/ExecutionPath.py
janis_core/ingestion/galaxy/gxtool/command/epath/ExecutionPathAnnotator.py
janis_core/ingestion/galaxy/gxtool/command/epath/__init__.py
janis_core/ingestion/galaxy/gxtool/command/epath/analysis.py
janis_core/ingestion/galaxy/gxtool/command/tokens/__init__.py
janis_core/ingestion/galaxy/gxtool/command/tokens/factory.py
janis_core/ingestion/galaxy/gxtool/command/tokens/prioritisation.py
janis_core/ingestion/galaxy/gxtool/command/tokens/token.py
janis_core/ingestion/galaxy/gxtool/command/tokens/utils.py
janis_core/ingestion/galaxy/gxtool/model/__init__.py
janis_core/ingestion/galaxy/gxtool/model/citations.py
janis_core/ingestion/galaxy/gxtool/model/configfile.py
janis_core/ingestion/galaxy/gxtool/model/metadata.py
janis_core/ingestion/galaxy/gxtool/model/requirement.py
janis_core/ingestion/galaxy/gxtool/model/script.py
janis_core/ingestion/galaxy/gxtool/model/tests.py
janis_core/ingestion/galaxy/gxtool/model/tool.py
janis_core/ingestion/galaxy/gxtool/model/params/__init__.py
janis_core/ingestion/galaxy/gxtool/model/params/input_param.py
janis_core/ingestion/galaxy/gxtool/model/params/output_param.py
janis_core/ingestion/galaxy/gxtool/model/params/param.py
janis_core/ingestion/galaxy/gxtool/model/params/param_register.py
janis_core/ingestion/galaxy/gxtool/parsing/__init__.py
janis_core/ingestion/galaxy/gxtool/parsing/inputs.py
janis_core/ingestion/galaxy/gxtool/parsing/main.py
janis_core/ingestion/galaxy/gxtool/parsing/outputs.py
janis_core/ingestion/galaxy/gxtool/parsing/param_flattener.py
janis_core/ingestion/galaxy/gxtool/parsing/tests/TestFactoryOld.py
janis_core/ingestion/galaxy/gxtool/parsing/tests/__init__.py
janis_core/ingestion/galaxy/gxtool/parsing/tests/checks.py
janis_core/ingestion/galaxy/gxtool/parsing/tests/custom_ops.py
janis_core/ingestion/galaxy/gxtool/parsing/tests/custom_preprocessors.py
janis_core/ingestion/galaxy/gxtool/parsing/tests/mapper.py
janis_core/ingestion/galaxy/gxtool/text/__init__.py
janis_core/ingestion/galaxy/gxtool/text/utils.py
janis_core/ingestion/galaxy/gxtool/text/cheetah/__init__.py
janis_core/ingestion/galaxy/gxtool/text/cheetah/blocks.py
janis_core/ingestion/galaxy/gxtool/text/cheetah/evaluation.py
janis_core/ingestion/galaxy/gxtool/text/simplification/__init__.py
janis_core/ingestion/galaxy/gxtool/text/simplification/aliases.py
janis_core/ingestion/galaxy/gxtool/text/simplification/filters.py
janis_core/ingestion/galaxy/gxtool/text/simplification/main_statement.py
janis_core/ingestion/galaxy/gxtool/text/simplification/simplify.py
janis_core/ingestion/galaxy/gxworkflow/__init__.py
janis_core/ingestion/galaxy/gxworkflow/connections/__init__.py
janis_core/ingestion/galaxy/gxworkflow/connections/scatter.py
janis_core/ingestion/galaxy/gxworkflow/parsing/__init__.py
janis_core/ingestion/galaxy/gxworkflow/parsing/inputs.py
janis_core/ingestion/galaxy/gxworkflow/parsing/metadata.py
janis_core/ingestion/galaxy/gxworkflow/parsing/step.py
janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/__init__.py
janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/metadata.py
janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/outputs.py
janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/prepost.py
janis_core/ingestion/galaxy/gxworkflow/parsing/tool_step/tool.py
janis_core/ingestion/galaxy/gxworkflow/tool_state/__init__.py
janis_core/ingestion/galaxy/gxworkflow/tool_state/filters.py
janis_core/ingestion/galaxy/gxworkflow/tool_state/load.py
janis_core/ingestion/galaxy/gxworkflow/updates/__init__.py
janis_core/ingestion/galaxy/gxworkflow/updates/arrays.py
janis_core/ingestion/galaxy/gxworkflow/updates/datatypes.py
janis_core/ingestion/galaxy/gxworkflow/updates/main.py
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janis_core/ingestion/galaxy/gxworkflow/values/connection.py
janis_core/ingestion/galaxy/gxworkflow/values/default.py
janis_core/ingestion/galaxy/gxworkflow/values/factory.py
janis_core/ingestion/galaxy/gxworkflow/values/runtime.py
janis_core/ingestion/galaxy/gxworkflow/values/scripts.py
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janis_core/ingestion/galaxy/gxwrappers/downloads/__init__.py
janis_core/ingestion/galaxy/gxwrappers/downloads/cache.py
janis_core/ingestion/galaxy/gxwrappers/downloads/wrappers.py
janis_core/ingestion/galaxy/gxwrappers/requests/__init__.py
janis_core/ingestion/galaxy/gxwrappers/requests/versions.py
janis_core/ingestion/galaxy/gxwrappers/scraping/__init__.py
janis_core/ingestion/galaxy/gxwrappers/scraping/repositories.py
janis_core/ingestion/galaxy/gxwrappers/scraping/revisions.py
janis_core/ingestion/galaxy/gxwrappers/scraping/scraping.py
janis_core/ingestion/galaxy/gxwrappers/scraping/single.py
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janis_core/ingestion/galaxy/gxwrappers/scraping/wrappers.py
janis_core/ingestion/galaxy/gxwrappers/wrappers/Wrapper.py
janis_core/ingestion/galaxy/gxwrappers/wrappers/WrapperCache.py
janis_core/ingestion/galaxy/gxwrappers/wrappers/__init__.py
janis_core/ingestion/galaxy/internal_mapping/__init__.py
janis_core/ingestion/galaxy/internal_mapping/main.py
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janis_core/ingestion/galaxy/internal_model/protocols.py
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janis_core/ingestion/galaxy/internal_model/tool/generate.py
janis_core/ingestion/galaxy/internal_model/tool/outputs.py
janis_core/ingestion/galaxy/internal_model/tool/tool.py
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janis_core/ingestion/galaxy/internal_model/workflow/input.py
janis_core/ingestion/galaxy/internal_model/workflow/metadata.py
janis_core/ingestion/galaxy/internal_model/workflow/workflow.py
janis_core/ingestion/galaxy/internal_model/workflow/registers/StepInputRegister.py
janis_core/ingestion/galaxy/internal_model/workflow/registers/StepOutputRegister.py
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janis_core/ingestion/galaxy/internal_model/workflow/step/__init__.py
janis_core/ingestion/galaxy/internal_model/workflow/step/inputs.py
janis_core/ingestion/galaxy/internal_model/workflow/step/metadata.py
janis_core/ingestion/galaxy/internal_model/workflow/step/outputs.py
janis_core/ingestion/galaxy/internal_model/workflow/step/post_step.txt
janis_core/ingestion/galaxy/internal_model/workflow/step/step.py
janis_core/ingestion/galaxy/janis_mapping/__init__.py
janis_core/ingestion/galaxy/janis_mapping/general.py
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janis_core/ingestion/galaxy/janis_mapping/workflow.py
janis_core/ingestion/galaxy/messages/__init__.py
janis_core/ingestion/galaxy/messages/logs.py
janis_core/ingestion/galaxy/messages/messages.py
janis_core/ingestion/galaxy/regex_to_glob/__init__.py
janis_core/ingestion/galaxy/regex_to_glob/common.py
janis_core/ingestion/galaxy/regex_to_glob/convert.py
janis_core/ingestion/galaxy/regex_to_glob/patterns.py
janis_core/ingestion/galaxy/runtime/__init__.py
janis_core/ingestion/galaxy/runtime/dates.py
janis_core/ingestion/galaxy/runtime/exceptions.py
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janis_core/ingestion/galaxy/runtime/tool.py
janis_core/ingestion/galaxy/runtime/startup/__init__.py
janis_core/ingestion/galaxy/runtime/startup/tool.py
janis_core/ingestion/galaxy/runtime/startup/workflow.py
janis_core/ingestion/galaxy/tags/__init__.py
janis_core/ingestion/galaxy/tags/groups.py
janis_core/ingestion/galaxy/tags/manager.py
janis_core/ingestion/galaxy/tags/rules.py
janis_core/ingestion/galaxy/tags/strategies.py
janis_core/ingestion/galaxy/utils/__init__.py
janis_core/ingestion/galaxy/utils/galaxy.py
janis_core/ingestion/galaxy/utils/general.py
janis_core/ingestion/wdl/__init__.py
janis_core/ingestion/wdl/main.py
janis_core/messages/__init__.py
janis_core/messages/config.yaml
janis_core/messages/logfile.py
janis_core/messages/main.py
janis_core/operators/__init__.py
janis_core/operators/logical.py
janis_core/operators/operator.py
janis_core/operators/selectors.py
janis_core/operators/standard.py
janis_core/operators/stringformatter.py
janis_core/redefinitions/__init__.py
janis_core/redefinitions/types.py
janis_core/redefinitions/utils.py
janis_core/redefinitions/tools/__init__.py
janis_core/redefinitions/tools/addbamstats.py
janis_core/redefinitions/tools/bcftools.py
janis_core/redefinitions/tools/bedtoolsgenomecoverage.py
janis_core/redefinitions/tools/bgzip.py
janis_core/redefinitions/tools/bioinformaticstool.py
janis_core/redefinitions/tools/bwamem_samtoolsview.py
janis_core/redefinitions/tools/cat.py
janis_core/redefinitions/tools/combinevariants.py
janis_core/redefinitions/tools/cutadapt.py
janis_core/redefinitions/tools/echo.py
janis_core/redefinitions/tools/fastqc.py
janis_core/redefinitions/tools/gatk4.py
janis_core/redefinitions/tools/generate.py
janis_core/redefinitions/tools/gridss.py
janis_core/redefinitions/tools/manta.py
janis_core/redefinitions/tools/parse.py
janis_core/redefinitions/tools/performancesummary.py
janis_core/redefinitions/tools/petermacutils.py
janis_core/redefinitions/tools/samtools.py
janis_core/redefinitions/tools/splitmultiallele.py
janis_core/redefinitions/tools/strelka.py
janis_core/redefinitions/tools/tabix.py
janis_core/redefinitions/tools/trimiupac.py
janis_core/redefinitions/tools/uncompressarchive.py
janis_core/redefinitions/tools/vardict.py
janis_core/redefinitions/tools/vcftools.py
janis_core/redefinitions/workflows/__init__.py
janis_core/redefinitions/workflows/addbamstats.py
janis_core/redefinitions/workflows/bioinformaticsworkflow.py
janis_core/redefinitions/workflows/bwaaligner.py
janis_core/redefinitions/workflows/gatkbaserecalbqsr.py
janis_core/redefinitions/workflows/gatkgermlinevariantcaller.py
janis_core/redefinitions/workflows/illuminagermlinevariantcaller.py
janis_core/redefinitions/workflows/mergeandmark.py
janis_core/redefinitions/workflows/performancesummarygenome.py
janis_core/redefinitions/workflows/vardictgermlinevariantcaller.py
janis_core/redefinitions/workflows/wgsgermline.py
janis_core/settings/__init__.py
janis_core/settings/datatypes.py
janis_core/settings/graph.py
janis_core/settings/testing.py
janis_core/settings/validation.py
janis_core/settings/ingest/__init__.py
janis_core/settings/ingest/cwl.py
janis_core/settings/ingest/galaxy.py
janis_core/settings/ingest/general.py
janis_core/settings/translate/__init__.py
janis_core/settings/translate/general.py
janis_core/settings/translate/nextflow.py
janis_core/tests/__init__.py
janis_core/tests/test_commandtool.py
janis_core/tests/test_conditionals.py
janis_core/tests/test_generics_util.py
janis_core/tests/test_ingestion_cwl.py
janis_core/tests/test_ingestion_galaxy.py
janis_core/tests/test_ingestion_wdl.py
janis_core/tests/test_janis_translate.py
janis_core/tests/test_logger.py
janis_core/tests/test_metadata.py
janis_core/tests/test_operators.py
janis_core/tests/test_python_tool.py
janis_core/tests/test_receivefrom.py
janis_core/tests/test_running.py
janis_core/tests/test_secondary.py
janis_core/tests/test_step.py
janis_core/tests/test_stringbuilder.py
janis_core/tests/test_test_runner.py
janis_core/tests/test_tools.py
janis_core/tests/test_translation_cwl.py
janis_core/tests/test_translation_modules.py
janis_core/tests/test_translation_nextflow.py
janis_core/tests/test_translation_wdl.py
janis_core/tests/test_types.py
janis_core/tests/test_validateinputvalue.py
janis_core/tests/test_validators.py
janis_core/tests/test_workflow.py
janis_core/tests/tests_util.py
janis_core/tests/data/aln.sam
janis_core/tests/data/aln.sorted.bam
janis_core/tests/data/aln.sorted.bam.bai
janis_core/tests/data/mutant_R1.fastq
janis_core/tests/data/test.txt
janis_core/tests/data/test_diff.txt
janis_core/tests/data/wildtype.fna
janis_core/tests/data/cwl/tools/BasicTestTool.cwl
janis_core/tests/data/cwl/tools/bwamem.cwl
janis_core/tests/data/cwl/tools/echo.cwl
janis_core/tests/data/cwl/tools/fastqc.cwl
janis_core/tests/data/cwl/tools/fastqc2.cwl
janis_core/tests/data/cwl/tools/gatk_haplotype_caller.cwl
janis_core/tests/data/cwl/tools/gatk_haplotype_caller_long.cwl
janis_core/tests/data/cwl/tools/rename_png.cwl
janis_core/tests/data/cwl/tools/rose.cwl
janis_core/tests/data/cwl/tools/samtools_flagstat.cwl
janis_core/tests/data/cwl/tools/datatypes/array_types.cwl
janis_core/tests/data/cwl/tools/datatypes/basic_types.cwl
janis_core/tests/data/cwl/tools/datatypes/secondary_types.cwl
janis_core/tests/data/cwl/tools/expressions/inputs_arguments.cwl
janis_core/tests/data/cwl/tools/expressions/outputs.cwl
janis_core/tests/data/cwl/tools/expressions/requirements.cwl
janis_core/tests/data/cwl/tools/expressions/resources.cwl
janis_core/tests/data/cwl/tools/expressions/streams.cwl
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janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/unite_protein_predictions.py
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/Dockerfile
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janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/CGC/combined_gene_caller_conf.json
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janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Combined_gene_caller/files/100000_130095.fasta.prodigal
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janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/expected-output/test_slim
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/GO-slim/owltools/owltools
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janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-apps.yaml
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-protein_formats.yaml
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/InterProScan/InterProScan-v5-none_docker.cwl
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janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/Pfam-Parse/pfam_annotations.cwl
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janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/Dockerfile
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janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/biom-convert.cwl
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janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/biom-convert_test.yml
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/empty_tax.cwl
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/empty_tax.sh
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/empty_tax.yml
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert/test-mapseq.hdf5
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert/test-mapseq.json
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/biom-convert/test-mapseq.tsv
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/biom-convert/expected_output/empty_tax/empty.html
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janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/cmsearch/infernal-cmsearch-v1.1.2.cwl
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janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-index.sh
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-sfetch-index-test.yml
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-sfetch-index.cwl
janis_core/tests/data/cwl/workflows/ebi-metagenomics/tools/RNA_prediction/easel/esl-sfetch-manyseqs-test.yml
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janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_averaged_structures.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_averaged_unp_domains.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_chopped_structs_unp_domains.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/avg_chopped_structures_unp_domains.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/bam_index.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/calc_chunking_number.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/carveme.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/carveme_files_to_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/cat.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/cat_models.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/check_alignment_scores.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/check_threshold_step.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/check_value.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chinking_SC_fasta_nucleotide.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chinking_fasta_nucleotide.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chinking_fasta_proteins.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chop_structs.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chunking_fasta.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/chunking_tsv.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/classifications_to_otu_counts.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/clean_classification.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/clean_fasta_headers.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/clean_headers.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/cmsearch.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/collect_lost_instances.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/combine.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/combine_ips.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/combine_trimmed.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compare_instances_CATH_Pfam.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress_carveme.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress_mapseq.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compress_prodigal.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compression.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/compression_func_ann.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/conversion.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/convert_trimmed_reads_to_fasta.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/copy_avg_dom.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_ITS_seqs.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_cds.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_lines_mapseq.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_lsu_fasta.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_masked_fasta.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_overlapped_reads.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_processed_reads.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_reads.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_reads_after_filtering.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_ssu_fasta.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_submitted_reads.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/count_submitted_reads_single.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/counts_to_hdf5.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/counts_to_json.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/create_csv_gp.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/create_csv_kp.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/create_new_parameters.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/crossmapping_CATH2Pfam.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/crossmapping_Pfam2CATH.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/diamond_run.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/eggnog_annotation.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/eggnog_homology_searches.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/expressiontool_bam_index.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_coords.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_sequences.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_subunits.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/extract_subunits_coords.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fasta_index.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fastqc.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fastqc_files_to_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_cath_structures.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_contigs_antismash.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_paired.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/filter_pfam_structures.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fix_embl_and_gbk.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/fix_geneclusters_txt.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/folder_compression.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/format_core_list.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/functional_stats.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gather_domain_like.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gather_failed_domains.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gemstats.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/genome_properties.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/get_coords.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/get_family_ids.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/get_ncrnas.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gff.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/go_summary.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_LSU.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_SSU.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_files.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzip_masked_ITS.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzipped_embl.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/gzipped_gbk.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hashsum.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hashsum_paired.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hashsum_single.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/header_addition.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/hmmsearch.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/index_reads.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/interproscan.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/join.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/kegg_pathways.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/kofamscan.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/length_filter.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/make_tab_sep.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/mapseq.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/mask_for_ITS.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/memote_files_to_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/memote_report_snapshot.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/memote_run.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/motus_classification.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_antismash_summary_to_pathways_systems_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_to_functional_annotation_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_to_pathways_systems_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/move_to_seq_cat_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/ngtax.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/ngtax_files_to_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/ngtax_to_tsv_fasta.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/no_tax_file_flag.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/overlap_reads.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/pairwise_align_avg_structs.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/parsing_hmmscan.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/per_dom_instance.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/per_unp_dom_instance.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/pfam.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/phyloseq_files_to_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/picrust2.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/picrust_files_to_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/pilon.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/post_processing.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/prodigal.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/prodigal_files_to_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/qc_stats.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/readmapping_pilon.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/reads_to_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/reformat_coords.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/remove_overlaps.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/rename_contigs.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/rename_geneclusters.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/rename_ncrnas.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/resmapping_for_CATH_PDB2UP.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/resmapping_for_Pfam_UP2PDB.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_antismash_in_folder.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_its_dir.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_output_dir.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_seq_dir.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/return_tax_dir.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_antismash.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_concatenate_deoverlapped_matches.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_concatenate_matches.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/run_quality_control_filtering.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/sam_to_sorted_bam.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/smetana.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/sorting.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/split_fasta.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/split_seqs.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/suppress_tax.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/tab_modification.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/tohdt.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_empty_fasta.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_file_flag.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_no_antismash_flag.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/touch_no_cds_flag.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/trim_quality_control.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_embl.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_gbk.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_geneclusters_txt.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unite_seed_orthologs.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unzip.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unzip_merged_reads.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/unzip_single_reads.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/vcf_compress.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/visualize_otu_counts.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/modules/write_summaries.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/ITS.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/after_qc.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/antismash.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/avg_unp_domains.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/before_qc.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cath_domain_instances.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cgc.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/change_formats_and_names.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_for_CATH2Pfam.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_for_Pfam2CATH.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_for_core.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chop_and_avg_from_list.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chunking.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/chunking_final.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/classify_LSUs.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/classify_SSUs.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cmsearch_assembly.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/cmsearch_raw_data.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/combined_gene_caller.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/diamond.nf
janis_core/tests/data/cwl/workflows/kf-somatic-workflow/workflow/translated/subworkflows/eggnog.nf
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