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Bump version for release 5.4#969

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jfy133 merged 3 commits intodevfrom
bump-version-release-5.4
Jan 26, 2026
Merged

Bump version for release 5.4#969
jfy133 merged 3 commits intodevfrom
bump-version-release-5.4

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@jfy133 jfy133 commented Jan 26, 2026

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@jfy133 jfy133 marked this pull request as ready for review January 26, 2026 12:05
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github-actions Bot commented Jan 26, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b9e5562

+| ✅ 381 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 5.4.0
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • 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
  • 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 nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-01-26 13:20:48

d4straub
d4straub approved these changes Jan 26, 2026
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Is that now the nf-core pipeline with the most frequent releases in the last 6 month??

Version confusion I think.
Potentially tests fail because snaps need to be updated?

Comment thread CHANGELOG.md Outdated
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jfy133 commented Jan 26, 2026

Is that now the nf-core pipeline with the most frequent releases in the last 6 month??

Version confusion I think. Potentially tests fail because snaps need to be updated?

haha, maybe, but I think that is a good thing for reviewers ™️ ;)

@jfy133 @d4straub
Update CHANGELOG.md
b9e5562 
Co-authored-by: Daniel Straub <[email protected]>
@jfy133 jfy133 merged commit 63ecfcf into dev Jan 26, 2026
4 checks passed
@jfy133 jfy133 deleted the bump-version-release-5.4 branch January 26, 2026 13:19
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@mashehu mashehu mashehu approved these changes

@d4straub d4straub d4straub approved these changes

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@muabnezor muabnezor Awaiting requested review from muabnezor muabnezor is a code owner

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