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added s4pred module to pipeline#60

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vagkaratzas merged 3 commits into
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add-s4pred
Dec 2, 2025
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added s4pred module to pipeline#60
vagkaratzas merged 3 commits into
devfrom
add-s4pred

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@vagkaratzas

@vagkaratzas vagkaratzas commented Dec 2, 2025 •
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Closes #21

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)

@github-actions

github-actions Bot commented Dec 2, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0269bdd

+| ✅ 203 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/ci.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-proteinannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-proteinannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-proteinannotator_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-12-02 12:33:16

pinin4fjords
pinin4fjords reviewed Dec 2, 2025
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Comment thread workflows/proteinannotator.nf Outdated
Comment thread CHANGELOG.md Outdated
@heuermh

heuermh commented Dec 2, 2025

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@vagkaratzas @pinin4fjords

Please consider adding yourself to the contributors block in nextflow.config
#48

There is also an empty credits section in the readme
https://github.com/nf-core/proteinannotator/blob/dev/README.md#credits

@vagkaratzas

vagkaratzas commented Dec 2, 2025 •
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Thanks for the reviews @pinin4fjords and @heuermh!

@vagkaratzas @pinin4fjords

Please consider adding yourself to the contributors block in nextflow.config #48

There is also an empty credits section in the readme https://github.com/nf-core/proteinannotator/blob/dev/README.md#credits

Would be easier to do that in a branch straight from the pipeline instead of a fork.

Let's do that before the first release.

@vagkaratzas vagkaratzas merged commit 76e1a3e into dev Dec 2, 2025
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@vagkaratzas vagkaratzas deleted the add-s4pred branch December 2, 2025 14:12
@vagkaratzas vagkaratzas mentioned this pull request Feb 4, 2026
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@heuermh heuermh heuermh approved these changes

@pinin4fjords pinin4fjords Awaiting requested review from pinin4fjords

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Add s4pred

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@vagkaratzas @heuermh @pinin4fjords