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Merged
merged 8 commits into from
Jul 18, 2025
Merged

Update modules #624

merged 8 commits into from
Jul 18, 2025

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sofstam
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@sofstam sofstam commented Jul 11, 2025

This PR updates all modules except porechop/abi and samtools

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/taxprofiler 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).

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@sofstam sofstam changed the title Update all modules except proechop/abi and samtools Update modules Jul 11, 2025
@LilyAnderssonLee
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Please add this update to CHANGELOG.md and also include the changes of the software version changes.

LilyAnderssonLee
LilyAnderssonLee reviewed Jul 15, 2025
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modules/nf-core/krona/ktimporttaxonomy/main.nf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
krona: $VERSION
krona: \$(ktImportTaxonomy | grep -Po "(?<=KronaTools )[0-9.]+")
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Please double check if the krona version was correctly saved using this new line.

LilyAnderssonLee
LilyAnderssonLee reviewed Jul 15, 2025
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@sofstam
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sofstam commented Jul 15, 2025

@nf-core-bot fix linting

jfy133
jfy133 approved these changes Jul 17, 2025
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jfy133 commented Jul 17, 2025 •
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@sofstam to get the tests to pass, I think we need the template update in here AND then also a new snapshot to record the new version numbers to get the tests to pass

But I see no other explicit iissues though

@sofstam sofstam merged commit e8a9a45 into nf-core:dev Jul 18, 2025
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@LilyAnderssonLee LilyAnderssonLee LilyAnderssonLee left review comments

@jfy133 jfy133 jfy133 approved these changes

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@sofstam @nf-core-bot @LilyAnderssonLee @jfy133