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NEXTFLOW → CWL

Direct path from a Nextflow pipeline to a CWL Workflow + CommandLineTool set.

draft pipelinesource/nextflowtarget/cwl

Phases

/ subway map 12 phases
  1. summarize-nextflow
  2. nextflow-summary-to-cwl-interface
  3. nextflow-summary-to-cwl-data-flow
  4. summary-to-cwl-template
  5. summarize-cwl-tool loop
  6. implement-cwl-tool-step loop
  7. validate-cwl loop
  8. nextflow-test-to-cwl-test-plan
  9. implement-cwl-workflow-test
  10. validate-cwl
  11. run-workflow-test
  12. debug-cwl-workflow-output

Run this pipeline

/ stop-gap harness

Run this pipeline today via its assembled harness skill pipeline-nextflow-to-cwl — install once (setup), then in a Claude Code session: 

/foundry-skills:pipeline-nextflow-to-cwl

Each run gets its own ./<run-slug>/ working directory so artifacts stay namespaced and a second run won't clobber the first — the harness sets this up first (phase detail).

phases
12
auto casts
2
manual
10
loops
3

NEXTFLOW → CWL

Direct path. Lifted from docs/HARNESS_PIPELINES.md §“NEXTFLOW → CWL”.

NF brings real test fixtures, so nextflow-test-to-cwl-test-plan replaces the [branch] test-data-resolution chain that paper-sourced pipelines need.