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PAPER → GALAXY

Direct path from a paper to a Galaxy gxformat2 workflow. No CWL intermediate.

draft pipelinesource/papertarget/galaxy

Phases

/ subway map 11 phases
  1. summarize-paper
  2. freeform-summary-to-galaxy-interface
  3. freeform-summary-to-galaxy-data-flow
  4. compare-against-iwc-exemplar
  5. freeform-summary-to-galaxy-template
  6. advance-galaxy-draft-step loop
  7. branch test-data-resolution
    1. paper-to-test-data
    2. find-test-data
    3. user-supplied
  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-paper-to-galaxy — install once (setup), then in a Claude Code session: 

/foundry-skills:pipeline-paper-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
8
manual
3
loops
1

PAPER → GALAXY

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

summarize-paper now emits the shared freeform-summary handoff, so the interface, data-flow, and template phases are shared with interview-sourced starts.

The composed alternative PAPER → CWL → GALAXY is a runtime composition of paper-to-cwl followed by cwl-to-galaxy — open question whether to surface as a distinct pipeline note.