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Use nf-core interproscan instead of local version #67

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@vagkaratzas vagkaratzas commented Feb 2, 2026 •
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Closes #3

  • Using final version of IPS that still had conda support. Warnings/error bug have been fixed in the nf-core module. Drawback is it can only run single-threaded.
  • Metromap updated
  • End-to-end test updated

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).

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nf-core-bot commented Feb 2, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
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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github-actions bot commented Feb 2, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f8fdee9

+| ✅ 213 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 2026-02-03 13:57:29

erikrikarddaniel
erikrikarddaniel approved these changes Feb 3, 2026
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Looks good. One small comment and an even smaller suggestion.
I was a bit surprised to see that on the interproscan module is nf-core while the download and swf are local. I suppose you have a reason for this but having an nf-core swf would make it easier for other pipelines.

vagkaratzas and others added 3 commits February 3, 2026 13:54
@vagkaratzas @erikrikarddaniel
Update docs/usage.md
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Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
@vagkaratzas
fix identation
f8a95ad
@vagkaratzas
removed test-related line from output.md
f8fdee9
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vagkaratzas commented Feb 3, 2026

Looks good. One small comment and an even smaller suggestion. I was a bit surprised to see that on the interproscan module is nf-core while the download and swf are local. I suppose you have a reason for this but having an nf-core swf would make it easier for other pipelines.

I just copy-pasted from nf-core/funcscan. But to be honest it's better if I move to aria2 + untar already. What do you think?

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