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PAPER → GALAXY

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

draft source/papertarget/galaxy

Phases

/ subway map 12 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. freeform-summary-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-paper-to-galaxy — install once (run guide), then select it in your runtime: 

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

PAPER → GALAXY

Start with a methods or tool paper. Include available supplementary methods, linked code, sample and reference data, and reported results that identify the workflow’s steps, parameters, inputs, and outputs. Point to concrete test inputs and expected values when the publication provides them. Leave missing versions, data locations, and ambiguous operations explicit in the freeform-summary.md handoff.

Review the Galaxy interface and data-flow briefs against the paper before accepting the draft topology. Check input and output labels, collection shapes, step dependencies, and the IWC comparison notes. Track unsupported choices in the open-requirements ledger. Resolve tool details from an acceptable wrapper during the draft loop, and bring an uncomputable step back to topology repair instead of guessing its missing input.

For workflow tests, use paper-derived data and expected outputs where they are resolvable. If they are not, check suitable IWC or public fixtures, then supply the missing data yourself. Review galaxy-test-plan.yml for assumed labels, fixture provenance, assertions, and omissions before inspecting the assembled galaxy-workflow.gxwf-tests.yml.

Inspect galaxy-workflow.gxwf.yml, galaxy-workflow-validation-result.json, and workflow-test-result.json. Use the debug report to investigate a failing run. Treat test-definition-missing or not-run as missing runtime evidence, and report unresolved source or test gaps with the workflow.