mature-galaxy-workflow-for-iwc

Take one concrete gxformat2 workflow and prepare an inspectable IWC-oriented revision. This is a single cohesive maturation action: read the upstream policy, fill what the evidence supports, make obvious purpose-preserving generalizations, keep an existing test aligned, prepare the normal companion files, and explain both the edits and the decisions that remain open.

The workflow is the only required input. A summary, test, prior companions, ledger, and contributor context all improve the result but must not be prerequisites.

Procedure

1. Inventory the supplied evidence

• Read starting-galaxy-workflow.gxwf.yml as the source of truth.
• Use summary-galaxy-workflow.json when supplied, but reconcile it against the workflow and derive the same facts directly when it is absent.
• Discover each optional input explicitly. Preserve supplied tests and companion documents as edit baselines. Initialize open-requirements.ledger.yml with entries: [] when no ledger is supplied.
• Record which inputs were present in the report. Never describe an absent artifact as inspected.

2. Apply the pinned IWC policy

Read the bundled IWC review prompt and apply every applicable check. Treat its pinned revision as the upstream policy source for this run, record that revision in the report, and never imply that newer policy was evaluated.

For every checklist item, record exactly one status:

• pass — evidence shows the item was already satisfied;
• changed — this run made a supported correction;
• needs-user-input — a consequential choice lacks evidence; or
• not-applicable — with a specific reason.

Inspect the workflow metadata and annotation, input/output and promoted-output labels, folder/file naming recommendation, genericity, README, changelog, Dockstore paths and creators, workflow/test label agreement, and test-data placement. Cite the file and field or section used for every conclusion.

3. Make only supported edits

Apply clear mechanical corrections: human-readable names, descriptive annotations grounded in the graph, label synchronization, companion paths, and removal of obviously sample-specific naming. Generalize a hard-coded sample value or path only when its role is unambiguous and an input can replace it without changing scientific behavior.

Preserve unrelated regions byte-for-byte where practical. Do not change tool identity or version, graph topology, scientifically meaningful defaults, test strength, or assertions merely to satisfy style guidance.

Never invent creators, ORCIDs, citations, license choices, release history, scientific purpose, reference-data strategy, or durable URLs. Use iwc-publication-context only as supplied evidence. When evidence is missing, leave the relevant value unchanged or visibly unresolved, set the checklist item to needs-user-input, and append a focused ledger entry saying what decision or evidence would resolve it.

4. Keep the workflow and test coherent

When a supplied test exists, preserve every job input and assertion except for the smallest change required by a supported interface-label edit. Update test keys in the same run as the corresponding workflow labels. Do not weaken assertions or manufacture expected outputs.

When no test exists, emit no galaxy-workflow-test artifact. Record needs-user-input for the missing test and point to the existing Galaxy test-planning and implement-galaxy-workflow-test path. An absent optional output is an expected result here, not a successful test claim.

5. Prepare ordinary IWC companions

• Create or update a README from evidenced workflow purpose, valid inputs, and expected outputs. Preserve useful supplied material. State unknown comparisons or tutorial links as unresolved; do not invent them.
• Create or update the changelog, preserving existing history and adding only an evidence-backed entry. If the release cannot be chosen safely, make that a ledger item rather than fabricating a version history.
• Create or update .dockstore.yml and align its paths with the emitted filenames. Preserve existing metadata and copy creator information only from workflow metadata or supplied context. Missing authorship is unresolved, not a license to guess.

6. Report and hand off

Write iwc-maturation-report.md with the pinned IWC source revisions from the bundled references, supplied-input inventory, per-item status and evidence, concise before/after descriptions, unresolved ledger ids, and the exact emitted files. End with an explicit statement that this Mold did not run terminal validation or workflow tests and did not create or update a GitHub pull request.

The downstream path owns validate-galaxy-workflow, run-workflow-test, repair/retest, and publication automation.

Non-goals

• No Planemo execution or validation claim.
• No new expected test result or weakened assertion.
• No tool, topology, or scientific redesign without explicit evidence.
• No branch, pull request, comment, label, or other GitHub mutation.
• No publication-readiness or canonical-IWC claim.