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cwl-workflows

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Authors portable, strongly-typed bioinformatics pipelines in the Common Workflow Language (CWL v1.2) as CommandLineTool/Workflow/ExpressionTool documents, validated with cwltool and run at scale on Toil/Arvados/Calrissian. Use when deciding CWL (portability/provenance/regulated) vs Nextflow/WDL/Snakemake; declaring secondaryFiles for indexed companions (.bai/.fai/.dict/.tbi and the caret rule); putting resources/containers under requirements (must-hold) vs hints (advisory) to avoid silent OOM; choosing scatterMethod (dotproduct vs flat_/nested_crossproduct); preferring $(...) parameter refs over ${...} JavaScript for portability; pinning DockerRequirement images; or emitting a CWLProv provenance object for audited/clinical settings.

When to use

• Authoring CWL v1.2 pipelines
• Validating CWL documents with cwltool
• Running CWL workflows on Toil, Arvados, or Calrissian
• Declaring secondaryFiles for indexed companions
• Configuring resources and containers in requirements vs hints
• Choosing scatterMethod for parallelization
• Emitting CWLProv provenance objects
• Deciding between CWL and Nextflow/WDL/Snakemake

When not to use

• Authoring Nextflow pipelines
• Authoring WDL pipelines
• Authoring Snakemake pipelines
• Using cwltool for large-scale production execution

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