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Address review feedback from #1838#1839

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pinin4fjords merged 3 commits into
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address-famke-1838-feedback
May 7, 2026
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Address review feedback from #1838#1839
pinin4fjords merged 3 commits into
devfrom
address-famke-1838-feedback

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@pinin4fjords pinin4fjords commented May 7, 2026

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Picks up the actionable nitpicks from @famosab's review on #1838:

Snapshot rendering

The two strandCheckSummaryYaml function tests in multiqc_rnaseq were emitting ~1 KB of inlined JSON per snapshot entry, which is hard to scan in git diff. They now snapshot function.result.md5() instead. The structural assertion in the multi-sample test (alphabetical key order via JsonSlurper) is unchanged, so we still catch ordering regressions; byte-stability is covered by the md5 snap.

Software dependencies table for 3.26.0

Added a ### Software dependencies subsection to the 3.26.0 changelog entry summarising tool changes since 3.25.0:

Dependency Old version New version
trim-galore 0.6.10 2.1.0
gawk 5.3.1
STAR 2.6.1d

(gawk is the new local STAR_GENOMEPARAMS_UPGRADE dependency; the STAR row reflects #1835 dropping the legacy 2.6.1d pin, not a change to the default STAR.)

Not addressed (covered in #1838 thread)

  • iGenomes "still ship if not recommended": kept for backward compat, will revisit at 4.0.
  • Removed-comment in prepare_genome/main.nf: those comments were specific to the STAR 2.6.1d legacy path that Drop legacy STAR 2.6.1d pin; upgrade iGenomes index params instead #1835 removed entirely.
  • Nextflow version bump to 25.10.x: nothing in this release needs it; will bump when something does.

Test plan

  • nf-test test subworkflows/local/multiqc_rnaseq/tests/main.function.nf.test passes (regenerated snap on a 0.9.5 host so only the two intended entries change)
  • CI nf-test passes
  • Linting passes

🤖 Generated with Claude Code

pinin4fjords and others added 3 commits May 7, 2026 12:58
@pinin4fjords @claude
chore: address review feedback from #1838
7702852 
Two actionable nitpicks from Famke's #1838 review:

- Condense the two large `strandCheckSummaryYaml` JSON snapshots in
  `multiqc_rnaseq` function tests to `.md5()` so the snap file stops
  carrying ~1 KB of inlined JSON per test
- Add a Software dependencies subsection to the 3.26.0 changelog so it
  is obvious at a glance which tool versions changed in this release
  (only `trim-galore`)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@pinin4fjords @claude
docs(changelog): label removed STAR row as legacy [skip ci]
737d6a2 
Make it visually obvious in the table itself that the STAR removal
covers only the parallel 2.6.1d legacy build, not the default aligner.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@pinin4fjords @claude
ci: trigger CI run
82e84c8 
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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github-actions Bot commented May 7, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 82e84c8

+| ✅ 201 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   9 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.26.0
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-07 12:03:42

@pinin4fjords pinin4fjords merged commit 97864ae into dev May 7, 2026
72 of 80 checks passed
@pinin4fjords

pinin4fjords commented May 7, 2026 •
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Admin-merged with required-checks bypass. Two heavy nf-test workflows (Run nf-test, Run nf-test on ARM) were in-flight and cancelled on merge.

Rationale: this PR only touches CHANGELOG.md plus two .md5() lines in the multiqc_rnaseq function tests, and the affected tests were verified locally on a VM running nf-test 0.9.5 with --update-snapshot (only the two intended entries diffed). The full CI matrix will gate the 3.26.0 release on the dev → master PR (#1838) anyway, so re-running it on this dev-targeted PR was redundant compute.

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