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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/deepmutscan 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).

@MaximilianStammnitz MaximilianStammnitz added the documentation Improvements or additions to documentation label Nov 25, 2025
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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: 3.4.1.
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.

@MaximilianStammnitz
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apologies for the many PRs @mashehu, I will try to be a bit more patient with merges from now on

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mashehu commented Nov 25, 2025

no worries, keep them coming 🙂

@MaximilianStammnitz
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no worries, keep them coming 🙂

alright. re-merge it is then :-)

@MaximilianStammnitz MaximilianStammnitz merged commit e7a21ec into nf-core:dev Nov 25, 2025
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3 participants