From 34a7bdc409d24878cbb4f70b284dd0bac7002021 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 31 Jul 2026 03:04:15 +0000
Subject: [PATCH] Update j178/prek-action action to v3

---
 .github/workflows/changelog.yml                             | 2 +-
 .github/workflows/fix-linting.yml                           | 2 +-
 .github/workflows/lint-code.yml                             | 2 +-
 nf_core/pipeline-template/.github/workflows/fix_linting.yml | 2 +-
 nf_core/pipeline-template/.github/workflows/linting.yml     | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index dd5ff6e347..3ade34c813 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -85,7 +85,7 @@ jobs:
 
       - name: Run pre-commit rules with prek
         if: steps.file_changed.outputs.changed == 'TRUE'
-        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
+        uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
         continue-on-error: true
         with:
           extra-args: --config ${{ runner.temp }}/pre-commit-config.yaml --files CHANGELOG.md
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 4415e97907..738e69acd1 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -33,7 +33,7 @@ jobs:
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
+        uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
         continue-on-error: true
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 681c5563a5..f223f32b3f 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -22,6 +22,6 @@ jobs:
       - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Run prek
-        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
+        uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
diff --git a/nf_core/pipeline-template/.github/workflows/fix_linting.yml b/nf_core/pipeline-template/.github/workflows/fix_linting.yml
index 4c91656253..3a0ee37570 100644
--- a/nf_core/pipeline-template/.github/workflows/fix_linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/fix_linting.yml
@@ -37,7 +37,7 @@ jobs:
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
+        uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
         continue-on-error: true
 
       # indication that the linting has finished
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 80c7055ef1..42e7310058 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -17,7 +17,7 @@ jobs:
         uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       - name: Run prek
-        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
+        uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
 
   nf-core:
     runs-on: ubuntu-latest