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NEXTFLOW → GALAXY

Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.

draft pipelinesource/nextflowtarget/galaxy

Phases

/ subway map 13 phases
  1. summarize-nextflow
  2. nextflow-summary-to-galaxy-reference-data
  3. nextflow-summary-to-galaxy-interface
  4. nextflow-summary-to-galaxy-data-flow
  5. compare-against-iwc-exemplar
  6. nextflow-summary-to-galaxy-template
  7. advance-galaxy-draft-step loop
  8. branch test-data-resolution
    1. nextflow-to-test-data
    2. find-test-data
    3. user-supplied
  9. nextflow-test-to-galaxy-test-plan
  10. implement-galaxy-workflow-test
  11. validate-galaxy-workflow
  12. run-workflow-test
  13. debug-galaxy-workflow-output

Run this pipeline

/ stop-gap harness

Run this pipeline today via its assembled harness skill pipeline-nextflow-to-galaxy — install once (run guide), then select it in either runtime: 

Claude: /foundry-skills:pipeline-nextflow-to-galaxy
Codex:  $pipeline-nextflow-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
13
auto casts
12
manual
1
loops
1

NEXTFLOW → GALAXY

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

Replaces the prior-art hand-authored nf-to-galaxy skill — same goal, decomposed into Molds, validation-driven (gxwf static schema replaces the prose caveat catalog).