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Switch fix-linting to the hardened nf-core/actions reusable workflow - #4

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mashehu merged 1 commit into
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Oct 7, 2026
Merged

Switch fix-linting to the hardened nf-core/actions reusable workflow#4
mashehu merged 1 commit into
devfrom
patch

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@mashehu

@mashehu mashehu commented Oct 7, 2026

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This replaces the old fix-linting workflow (.github/workflows/fix_linting.yml, or .github/workflows/fix-linting.yml in pipelines created before nf-core/tools 3.3.0) with .github/workflows/fix-linting.yml, a short stub that calls the reusable fix-linting workflow from nf-core/actions (nf-core/tools#4485).

The old workflow ran the pull request's own lint hooks in a job that also held the nf-core-bot token. The reusable workflow checks who asked for the fix, runs the pull request's code without any secrets, and pushes the result from a separate job that never runs pull request code.

Commenting @nf-core-bot fix linting on a PR works as before. The next template sync makes the same change on dev.

@nf-core-bot

nf-core-bot commented Oct 7, 2026

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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: 3.5.2.
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.

@github-actions

github-actions Bot commented Oct 7, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d5e7cd9

+| ✅ 258 tests passed       |+
#| ❔   3 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/msproteomics/msproteomics/subworkflows/nf-core/dia_proteomics_analysis/main.nf: _ .combine(ch_speclib_in.ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/msproteomics/msproteomics/subworkflows/nf-core/dia_proteomics_analysis/main.nf: _ .combine(ch_empirical_library_in.ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/msproteomics/msproteomics/subworkflows/nf-core/dia_proteomics_analysis/main.nf: _ .combine(ch_empirical_log_in.ifEmpty(null))
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/msproteomics/msproteomics/subworkflows/nf-core/dia_proteomics_analysis/main.nf: _ // - combine with ifEmpty(null) pairs each input with either existing speclib or null
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/msproteomics/msproteomics/subworkflows/nf-core/dia_proteomics_analysis/main.nf: _ .combine(ch_speclib.ifEmpty(null))
    _

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-10-07 13:52:54

@mashehu
mashehu merged commit 3b965c2 into dev Oct 7, 2026
8 checks passed
@mashehu
mashehu deleted the patch branch October 7, 2026 13:54
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@mashehu @nf-core-bot