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Important! Template update for nf-core/tools v3.3.2 #235

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Important! Template update for nf-core/tools v3.3.2 #235

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@nf-core-bot nf-core-bot commented Jul 8, 2025

Version 3.3.2 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.3.2 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.3.2 release page.

@nf-core-bot nf-core-bot mentioned this pull request Jul 8, 2025
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github-actions bot commented Jul 9, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit ab9cfdd

+| ✅ 227 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌   4 tests failed       |-

❌ Test failures:

  • nf_test_content - 'tests/main.nf.test' does not contain outdir parameter, it should contain outdir = "$outputDir"
  • nf_test_content - 'tests/main.nf.test' does not snapshot a 'versions.yml' file
  • actions_nf_test - Minimum pipeline NF version '25.04.2' is not tested in '.github/workflows/nf-test.yml'
  • rocrate_readme_sync - The RO-Crate descriptions do not match the README.md content. Use nf-core pipelines lint --fix rocrate_readme_sync to update.

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-07-09 08:26:45

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nf-core-bot commented Oct 16, 2025

Version 3.4.1 of the nf-core/tools pipeline template has just been released. This pull-request is now outdated and has been closed in favour of #243

Please use #243 to merge in the new changes from the nf-core template as soon as possible.

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