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CWL → GALAXY

Path from a CWL Workflow to a Galaxy gxformat2 workflow. Lighter upstream extraction.

draft pipelinesource/cwltarget/galaxy

Phases

/ subway map 11 phases
  1. summarize-cwl
  2. cwl-summary-to-galaxy-interface
  3. cwl-summary-to-galaxy-data-flow
  4. compare-against-iwc-exemplar
  5. cwl-summary-to-galaxy-template
  6. advance-galaxy-draft-step loop
  7. cwl-test-to-galaxy-test-plan
  8. implement-galaxy-workflow-test
  9. validate-galaxy-workflow
  10. run-workflow-test
  11. debug-galaxy-workflow-output

Run this pipeline

/ stop-gap harness

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

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

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
11
auto casts
9
manual
2
loops
1

CWL → GALAXY

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

CWL is already structured, so the upstream summarize-cwl → cwl-summary-to-galaxy-interface → cwl-summary-to-galaxy-data-flow chain is much lighter than its Nextflow counterpart. The per-step Galaxy authoring tier downstream is identical to the other Galaxy-targeting pipelines.