diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index a0d9c69..8176eb1 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -31,22 +31,15 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      # Install and run pre-commit
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6
-        with:
-          python-version: 3.11
-
-      - name: Install pre-commit
-        run: pip install pre-commit
-
-      - name: Run pre-commit
-        id: pre-commit
-        run: pre-commit run --all-files
+      # Run prek (drop-in, faster pre-commit; reads the same
+      # .pre-commit-config.yaml). The action runs `prek run --all-files`.
+      - uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4
+        id: prek
         continue-on-error: true
 
       # indication that the linting has finished
       - name: react if linting finished succesfully
-        if: steps.pre-commit.outcome == 'success'
+        if: steps.prek.outcome == 'success'
         uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
         with:
           comment-id: ${{ github.event.comment.id }}
@@ -54,7 +47,7 @@ jobs:
 
       - name: Commit & push changes
         id: commit-and-push
-        if: steps.pre-commit.outcome == 'failure'
+        if: steps.prek.outcome == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
index 4cf10b5..1bc21f8 100644
--- a/.github/workflows/pre-commit.yml
+++ b/.github/workflows/pre-commit.yml
@@ -10,11 +10,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6
-        with:
-          python-version: 3.11
-      - name: Install pre-commit
-        run: pip install pre-commit
-
-      - name: Run pre-commit
-        run: pre-commit run --all-files
+      # prek is a drop-in, faster reimplementation of pre-commit; it reads the
+      # existing .pre-commit-config.yaml and runs the same hooks.
+      - uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4