wf2wf DocumentationΒΆ
Welcome to wf2wf β 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!
Overview πΒΆ
wf2wf
converts workflows between any supported engines via a loss-preserving Intermediate Representation (IR). Supported today:
β’ Snakemake β’ CWL β’ Nextflow β’ WDL β’ Galaxy β’ HTCondor DAGMan (+ BioCompute Objects)
Key features:
π Universal conversion β always A β IR β B for maximum fidelity.
𧬠Loss mapping β records unexpressed fields in side-cars so nothing vanishes.
π³ Environment automation β Conda β OCI β Apptainer with SBOM generation.
β Regulatory support β Emits BioCompute Objects and provenance metadata.
Quick installΒΆ
pip install wf2wf # or: conda install -c conda-forge wf2wf
Quick CLI tour πΒΆ
# Convert Snakemake β DAGMan and build container images
wf2wf convert -i Snakefile -o pipeline.dag --auto-env build --interactive
# Convert CWL β Nextflow, aborting on information loss
wf2wf convert -i analysis.cwl -o main.nf --out-format nextflow --fail-on-loss
SectionsΒΆ
User Guide β step-by-step tutorials and best practices.
CLI Reference β exhaustive help for every command.
Developer Guide β IR schema, environment pipeline, contributor tips.
Changelog β project history and release notes.