Stop run-workflow-test guessing a Galaxy branch#363
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Mold left the Galaxy version unspecified; a run filled the vacuum with --galaxy_branch release_25.0, which rejected the workflow at invocation. Add explicit no-pin rule to the Mold and record planemo's master default in the architecture note. No new frontmatter field, no pinned release - a pin would go stale and reproduce this on a slower clock. Recast the five casts bundling the note. freeform-summary-to-galaxy-test-plan also picks up a pre-existing stale schema reconciliation. Closes #361 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Closes #361.
Problem
The sarek run authored a workflow with
sample_sheets, then tested it against Galaxyrelease_25.0. Tracing it back (thanks @mvdbeek), the branch was introduced by the phase-12 agent when it generatedrun-planemo.sh— not by a planemo default, a Foundry source note, or an earlier artifact. Therun-workflow-testMold left the Galaxy version entirely unspecified, and the agent filled the vacuum with a guess.Fix
Close the vacuum, minimally.
content/molds/run-workflow-test/index.md— new step 3: leave--galaxy_branchoff unless the user or harness supplied one, never guess arelease_*, and record a supplied branch in the output so a later failure can be read against it.content/research/planemo-workflow-test-architecture.md— one factual line under managed-mode behavior:--galaxy_branchdefaults tomaster, so omitting it tests newest; naming an older release narrows accepted workflow syntax and the rejection surfaces as an invocation-time error rather than a version mismatch. Five Molds load this note on demand, so the fact also lands where a debug pass looks.Deliberately not done: no
galaxy_branchfrontmatter field, no version-resolution logic, no pinned release anywhere. A pin would go stale and reproduce this bug on a slower clock.Casts
Recast the five bundles carrying the note.
freeform-summary-to-galaxy-test-planalso picks up a pre-existing stale schema reconciliation (thegalaxysource-family enum, already inmain's package — that cast just hadn't been re-run).Checks
npm run validate— 0 errors.make check-assemble-pipelines— clean.npm run testhas 2 failures intests/cast-mold.test.ts(summarize-nextflowschema drift). These are pre-existing onmain, confirmed by stashing and re-running; untouched here.🤖 Generated with Claude Code