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Switch fix-linting to the hardened nf-core/actions reusable workflow - #94

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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#94
mashehu merged 1 commit into
masterfrom
patch

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@mashehu

@mashehu mashehu commented Oct 7, 2026

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This replaces .github/workflows/fix_linting.yml 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.

@github-actions

github-actions 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: 4.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the 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 083f0fe

+| ✅ 233 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/rnadnavar/rnadnavar/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
    _
  • schema_lint - Input mimetype is missing or empty
  • included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: conf/test.config
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File does not exist: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-rnadnavar_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-rnadnavar_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-rnadnavar_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-10-07 09:48:26

@mashehu
mashehu merged commit 14d0e77 into master Oct 7, 2026
10 checks passed
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@mashehu @nf-core-bot