Clean up convert-nfcore + planemo-fork residue after base-planemo pin

[jmchilton]

Posted by Claude (AI assistant) on behalf of @jmchilton — not authored by them personally.

Follow-up to 60e180e, which pinned the shared [[planemo]] note to base released planemo==0.75.44 (off the jmchilton/planemo@a9b8b8b… fork). That fixed the invalid cast install command (uv tool install planemo==git+https://…) for the workflow-test phases, but deliberately left several things on the fork that still need cleanup once planemo cuts a release carrying the fork-only subcommands.

Background

The fork SHA added planemo cli_metadata and planemo output_schema (galaxyproject/planemo#1636). The nextflow→galaxy tool-conversion path (convert-nfcore-module-to-galaxy-tool) and the vendored-artifact regeneration story depend on those subcommands, so they can't move to base planemo yet.

Residue to clean up

1. convert-nfcore-module-to-galaxy-tool cast is stale and needs a re-condense + recast. Independent of planemo, its source research notes drifted (6 notes, last edited 2026-06-10) and migrated pattern → research; a fresh cast moves the bundle's ref paths references/patterns/ → references/notes/ but the condensed files require the two-phase LLM re-condense the plain cast can't do. cast 60e180e reverted this Mold's cast to avoid shipping dangling refs. Needs a proper re-condense pass.

   • Notes: content/research/nfcore-{channel-input-to-galaxy-collection,meta-map-to-galaxy-params,stub-block-to-galaxy-noop-test,task-ext-args-to-galaxy-additional-options,versions-emit-to-galaxy-version-command}.md, galaxy-discover-datasets.md.

2. Its standalone cast still bundles the fork planemo.md, now inconsistent with the base source note. Will resolve when (1) re-casts — but only correct after a base planemo release has #1636, else convert-nfcore loses cli_metadata/output_schema.

3. Fork SHA still pinned across vendored artifacts + planemo subcommand notes (move to the released pin once #1636 ships):

   • packages/planemo-cli-meta/ (src/cli-meta.provenance.json, …provenance.generated.ts, scripts/sync-from-planemo.mjs)
   • packages/planemo-test-report-schema/ (src/test-report.provenance.json, …provenance.generated.ts, scripts/sync-from-planemo.mjs)
   • content/cli/planemo/planemo-{cli_metadata,output_schema,test,lint,workflow_test_init,workflow_test_on_invocation}.md
   • content/schemas/planemo-test-report.md
   • scripts/sync-planemo-cli.ts

4. Latent renderInstallCommand bug (packages/build-cli/src/lib/required-tools.ts): always emits <pkg>==<package_version>, which mangles any VCS (git+…) or range (>=x) pin into invalid syntax. Base-planemo dodges it, but it'll bite the next VCS/range-pinned pypi tool. Harden + unit-test.

Done-when

• A planemo release carrying #1636 exists, the pin flips to it everywhere above, vendored artifacts regenerate cleanly, and convert-nfcore re-condenses + recasts with a consistent base-or-release planemo install line.