wf2wf Documentation

Welcome to wf2wf – the universal workflow-format converter.

Docs in progress

This documentation site is still growing. If something is missing, please open an issue or contribute a pull request!

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Overview 🌐

wf2wf converts workflows between any supported engines via a loss-preserving Intermediate Representation (IR). Supported today:

• Snakemake • CWL • Nextflow • WDL • Galaxy • HTCondor DAGMan (+ BioCompute Objects)

Key features:

• 🔄 Universal conversion – always A → IR → B for maximum fidelity.

• 🧬 Loss mapping – records unexpressed fields in side-cars so nothing vanishes.

• 🐳 Environment automation – Conda → OCI → Apptainer with SBOM generation.

• ⚖ Regulatory support – Emits BioCompute Objects and provenance metadata.

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Quick install

pip install wf2wf            # or: conda install -c conda-forge wf2wf

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Quick CLI tour 🚀

# Convert Snakemake → DAGMan and build container images
wf2wf convert -i Snakefile -o pipeline.dag --auto-env build --interactive

# Convert CWL → Nextflow, aborting on information loss
wf2wf convert -i analysis.cwl -o main.nf --out-format nextflow --fail-on-loss

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Sections

• User Guide – step-by-step tutorials and best practices.

• CLI Reference – exhaustive help for every command.

• Developer Guide – IR schema, environment pipeline, contributor tips.

• Changelog – project history and release notes.