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feat: Add interproscan_run param#52

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olgabot merged 12 commits into
olgabot/add-interproscanfrom
ci-interproscan
Jun 3, 2025
Merged

feat: Add interproscan_run param#52
olgabot merged 12 commits into
olgabot/add-interproscanfrom
ci-interproscan

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@edmundmiller
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@edmundmiller edmundmiller commented Jun 3, 2025

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@edmundmiller edmundmiller requested a review from olgabot June 3, 2025 18:28
@edmundmiller edmundmiller self-assigned this Jun 3, 2025
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nf-core-bot commented Jun 3, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
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 Jun 3, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 738c11f

+| ✅ 180 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌   2 tests failed       |-
Details

❌ Test failures:

  • nextflow_config - Config default value incorrect: params.interproscan_tar_gz is set as http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.74.105/interproscan-5.74.105-64-bit.tar.gz in nextflow_schema.json but is https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.74-105.0/interproscan-5.74-105.0-64-bit.tar.gz in nextflow.config.
  • modules_json - Entry for /home/runner/work/proteinannotator/proteinannotator/modules/nf-core/interproscan found in modules.json but module is not installed in pipeline.

❗ 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
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.1
  • Run at 2025-06-03 19:26:53

olgabot
olgabot approved these changes Jun 3, 2025
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Looks good, thank you!

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olgabot commented Jun 3, 2025

Merging even though linting is failing, this is because of the #51 PR

@olgabot olgabot merged commit 62ab267 into olgabot/add-interproscan Jun 3, 2025
33 of 34 checks passed
@vagkaratzas vagkaratzas mentioned this pull request Feb 4, 2026
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