CWL + Docker Workflow

Overview

A workflow management approach that combines Common Workflow Language (CWL) for portable pipeline specification with Docker containers for reproducible execution environments. CWL describes tool inputs, outputs, and computational steps in a language-agnostic YAML/JSON format; Docker encapsulates software dependencies into isolated images. Together, they enable cloud-platform-independent reproducibility of bioinformatics pipelines.

Used by

• The TCGA MC3 somatic calling pipeline was distributed as a CWL + Docker workflow at https://github.com/OpenGenomics/mc3, enabling reproducible execution of the seven-caller ensemble across DNAnexus and other cloud platforms PMID:29596782

Notes

• CWL workflows are portable across compliant executors (cwltool, Toil, Cromwell, etc.) and cloud platforms (AWS, GCP, Azure, DNAnexus).
• Docker container versioning is critical for reproducibility; pinning image digests (not just tags) is recommended.
• The MC3 CWL release was intended as a reference implementation to enable other groups to replicate or extend the pipeline.

Sources

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