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CWL → GALAXY

Translate a CWL Workflow into a Galaxy gxformat2 workflow, then assemble and run a Galaxy workflow test.

draft source/cwltarget/galaxy

Phases

/ subway map 12 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. branch test-data-resolution
    1. cwl-to-test-data
    2. find-test-data
    3. user-supplied
  8. cwl-test-to-galaxy-test-plan
  9. implement-galaxy-workflow-test
  10. validate-galaxy-workflow
  11. run-workflow-test
  12. 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 (run guide), then select it in your runtime: 

Claude:      /foundry-skills:pipeline-cwl-to-galaxy
Codex:       $pipeline-cwl-to-galaxy
Antigravity: /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
12
auto casts
11
manual
1
loops
1

CWL → GALAXY

Start with a CWL Workflow entrypoint and its referenced tools, supplied as a local path or HTTP(S) URL. Include available CWL job files and expected outputs so the Galaxy test can carry forward source test evidence. This path also accepts CWL produced by a paper-to-CWL or Nextflow-to-CWL run.

Follow the declared phases in order. Review the Galaxy interface and data-flow briefs before accepting the draft topology. Run advance-galaxy-draft-step until no drafty step remains, and resolve recorded gaps instead of guessing tool details. For test inputs, try the CWL source cases first, then search for suitable fixtures, then request user-supplied data if needed.

Check the concrete galaxy-workflow.gxwf.yml, its galaxy-workflow.gxwf-tests.yml companion, and workflow-test-result.json. Use the validation and debug phases to address reported failures. If the result is test-definition-missing or not-run, report the gap with the workflow instead of marking the translation verified.