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@olgabot olgabot commented Jan 10, 2026

  • Add eggnog-mapper module
  • Add Eggnog-mapper to main pipeline
  • Add eggNOG mapper database download and separate subworkflow

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/proteinannotator branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (e.g. nf-test test */local --profile=~test,docker for all new local tests).
  • Check for unexpected warnings in debug mode (nf-test test */local --profile=~test,docker,debug).
  • 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).
    • docs/images/proteinannotator-metromap.light.excalidraw.png and docs/images/proteinannotator-metromap.light.excalidraw.png (edit the light version only, then export and turn on dark mode) are both updated (use the excalidraw website or VS Code plugin to edit)

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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.

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@vagkaratzas vagkaratzas left a comment

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Is this PR ready for review?
Would be awesome to first push the eggnog_download_db module to nf-core/modules first, and then source from there. More eyes for reviewing and better maintenance :D

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4 participants