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[codex] Fix module Planemo refs and eval#244

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jmchilton merged 1 commit into
mainfrom
codex/module-planemo-eval-cleanup
May 12, 2026
Merged

[codex] Fix module Planemo refs and eval#244
jmchilton merged 1 commit into
mainfrom
codex/module-planemo-eval-cleanup

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Summary

  • Switch the convert-nfcore module Mold's Planemo command references from invalid condense mode to the current CLI command sidecar mode.
  • Replace placeholder Planemo lint/test manual sections with minimal factual notes and examples.
  • Add a small initial eval.md for the convert Mold focused on wrapper readiness and module fidelity.

Why

The convert Mold could not pass the deterministic cast check because cli-command references are currently emitted as structured sidecars, not condensed text. The Planemo command pages also still carried placeholder preserved sections, and the Mold lacked an eval file.

Validation

  • npm run validate passes with 0 errors; existing repository warnings remain.
  • npm run cast -- convert-nfcore-module-to-galaxy-tool --target=claude --check now reports 0 errors. It still reports expected drift for not-yet-generated cast outputs.
  • npm run check:planemo-cli was attempted but could not run because pinned planemo is not installed on PATH in this checkout.

@jmchilton
jmchilton marked this pull request as ready for review May 12, 2026 02:14
@jmchilton
jmchilton merged commit a675a52 into main May 12, 2026
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