From 80ecdbcaec450898eb91ec4b14e8e7ae61f6079f Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 7 Oct 2026 14:52:37 +0200
Subject: [PATCH] Switch fix-linting to the hardened nf-core/actions reusable
 workflow

---
 .github/workflows/fix-linting.yml | 98 +++++--------------------------
 1 file changed, 15 insertions(+), 83 deletions(-)

diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 3838bc30..81ac1812 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -1,89 +1,21 @@
 name: Fix linting from a comment
 on:
   issue_comment:
-    types: [created]
+    types: [created] # Add "@nf-core-bot fix linting" as a PR comment to trigger this workflow.
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.issue.number }}
 
 jobs:
   fix-linting:
-    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
-    if: >
-      contains(github.event.comment.html_url, '/pull/') &&
-      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'nf-core/multiplesequencealign'
-    runs-on: ubuntu-latest
-    steps:
-      # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-        with:
-          token: ${{ secrets.nf_core_bot_auth_token }}
-
-      # indication that the linting is being fixed
-      - name: React on comment
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
-        with:
-          comment-id: ${{ github.event.comment.id }}
-          reactions: eyes
-
-      # Action runs on the issue comment, so we don't get the PR by default
-      # Use the gh cli to check out the PR
-      - name: Checkout Pull Request
-        run: gh pr checkout ${{ github.event.issue.number }}
-        env:
-          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
-
-      # Install and run pre-commit
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.12"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
-
-      - name: Run pre-commit
-        id: pre-commit
-        run: pre-commit run --all-files
-        continue-on-error: true
-
-      # indication that the linting has finished
-      - name: react if linting finished succesfully
-        if: steps.pre-commit.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
-        with:
-          comment-id: ${{ github.event.comment.id }}
-          reactions: "+1"
-
-      - name: Commit & push changes
-        id: commit-and-push
-        if: steps.pre-commit.outcome == 'failure'
-        run: |
-          git config user.email "core@nf-co.re"
-          git config user.name "nf-core-bot"
-          git config push.default upstream
-          git add .
-          git status
-          git commit -m "[automated] Fix code linting"
-          git push
-
-      - name: react if linting errors were fixed
-        id: react-if-fixed
-        if: steps.commit-and-push.outcome == 'success'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
-        with:
-          comment-id: ${{ github.event.comment.id }}
-          reactions: hooray
-
-      - name: react if linting errors were not fixed
-        if: steps.commit-and-push.outcome == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
-        with:
-          comment-id: ${{ github.event.comment.id }}
-          reactions: confused
-
-      - name: react if linting errors were not fixed
-        if: steps.commit-and-push.outcome  == 'failure'
-        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
-        with:
-          issue-number: ${{ github.event.issue.number }}
-          body: |
-            @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
-            See [CI log](https://github.com/nf-core/multiplesequencealign/actions/runs/${{ github.run_id }}) for more details.
+    uses: nf-core/actions/.github/workflows/fix-linting.yml@v1
+    with:
+      nextflow-versions: '["25.10.4","latest-everything"]'
+    permissions:
+      actions: read
+      contents: read
+      issues: write
+      pull-requests: write
+
+    secrets:
+      BOT_TOKEN: ${{ secrets.nf_core_bot_auth_token }}