Bump tj-actions/changed-files from 23 to 41 in /.github/workflows

[dependabot]

Bumps tj-actions/changed-files from 23 to 41.

Release notes

Sourced from tj-actions/changed-files's releases.

v41

Changes in v41.0.1

What's Changed

• Upgraded to v41 by @​tj-actions-bot in tj-actions/changed-files#1811
• chore(deps): update dependency eslint-plugin-prettier to v5.1.2 by @​renovate in tj-actions/changed-files#1813
• fix: update characters escaped by safe output by @​jackton1 in tj-actions/changed-files#1815

Full Changelog: tj-actions/changed-files@v41...v41.0.1

---

Changes in v41.0.0

🔥 🔥 BREAKING CHANGE 🔥 🔥

A new safe_output input is now available to prevent outputting unsafe filename characters (Enabled by default). This would escape characters in the filename that could be used for command injection.

[!NOTE] This can be disabled by setting the safe_output to false this comes with a recommendation to store all outputs generated in an environment variable first before using them.

Example

...
    - name: Get changed files
      id: changed-files
      uses: tj-actions/changed-files@v40
      with:
        safe_output: false # set to false because we are using an environment variable to store the output and avoid command injection.
- name: List all added files
  env:
    ADDED_FILES: ${{ steps.changed-files.outputs.added_files }}
  run: |
    for file in "$ADDED_FILES"; do
      echo "$file was added"
    done

...

What's Changed

• chore(deps): update typescript-eslint monorepo to v6.15.0 by @​renovate in tj-actions/changed-files#1801
• Upgraded to v40.2.3 by @​tj-actions-bot in tj-actions/changed-files#1800
• chore(deps): update dependency eslint-plugin-prettier to v5.1.0 by @​renovate in tj-actions/changed-files#1802
• chore(deps): lock file maintenance by @​renovate in tj-actions/changed-files#1803
• chore(deps): update dependency eslint-plugin-prettier to v5.1.1 by @​renovate in tj-actions/changed-files#1804
• fix: update safe output regex and the docs by @​tj-actions-bot in tj-actions/changed-files#1805
• Revert "chore(deps): update actions/download-artifact action to v4" by @​jackton1 in tj-actions/changed-files#1806
• Update README.md by @​jackton1 in tj-actions/changed-files#1808

... (truncated)

Changelog

Sourced from tj-actions/changed-files's changelog.

Changelog

41.0.1 - (2023-12-24)

🐛 Bug Fixes

• Update characters escaped by safe output (#1815) (716b1e1) - (Tonye Jack)

⚙️ Miscellaneous Tasks

• deps: Update dependency eslint-plugin-prettier to v5.1.2 (7aaf10d) - (renovate[bot])

⬆️ Upgrades

• Upgraded to v41 (#1811)

Co-authored-by: jackton1 [email protected] (cc08e17) - (tj-actions[bot])

Commits

• 716b1e1 fix: update characters escaped by safe output (#1815)
• 7aaf10d chore(deps): update dependency eslint-plugin-prettier to v5.1.2
• cc08e17 Upgraded to v41 (#1811)
• 6e79d6e Update README.md
• d13ac19 Update README.md
• bb89f97 Update README.md
• 1864078 Updated README.md (#1810)
• f495a03 chore(deps): lock file maintenance
• 47371c5 Update README.md (#1808)
• 4f573fe Revert "chore(deps): update actions/download-artifact action to v4" (#1806)
• Additional commits viewable in compare view

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[github-actions]

This PR is against the master branch ❌

• Do not close this PR
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---

Hi @dependabot[bot],

It looks like this pull-request is has been made against the nf-core/tools master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/tools dev branch.

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (d52fda0) 75.01% compared to head (893fca6) 75.03%.
Report is 3 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2626      +/-   ##
==========================================
+ Coverage   75.01%   75.03%   +0.02%     
==========================================
  Files          85       85              
  Lines        9384     9384              
==========================================
+ Hits         7039     7041       +2     
+ Misses       2345     2343       -2     

☔ View full report in Codecov by Sentry.
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[mashehu]

Fixed in dev

[dependabot]

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