From 82815f9ebe540464e5a6edbd3c7a00c4daaa26e0 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Mon, 29 Jun 2026 12:56:18 +0000
Subject: [PATCH] Update GitHub Actions

---
 .github/workflows/branch.yml                                | 2 +-
 .github/workflows/changelog.yml                             | 6 +++---
 .github/workflows/create-lint-wf.yml                        | 2 +-
 .github/workflows/create-test-lint-wf-template.yml          | 2 +-
 .github/workflows/create-test-wf.yml                        | 2 +-
 .github/workflows/deploy-pypi.yml                           | 2 +-
 .github/workflows/fix-linting.yml                           | 2 +-
 .github/workflows/lint-code.yml                             | 2 +-
 .github/workflows/nextflow-source-test.yml                  | 4 ++--
 .github/workflows/pytest.yml                                | 2 +-
 .github/workflows/sync.yml                                  | 2 +-
 .github/workflows/update-template-snapshots.yml             | 2 +-
 .github/workflows/update-textual-snapshots.yml              | 2 +-
 .../pipeline-template/.github/actions/nf-test/action.yml    | 2 +-
 nf_core/pipeline-template/.github/workflows/branch.yml      | 2 +-
 .../.github/workflows/download_pipeline.yml                 | 2 +-
 nf_core/pipeline-template/.github/workflows/fix_linting.yml | 2 +-
 nf_core/pipeline-template/.github/workflows/linting.yml     | 4 ++--
 .../.github/workflows/template-version-comment.yml          | 2 +-
 19 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 240dc2dae0..addbc7bcbd 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -18,7 +18,7 @@ jobs:
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
+        uses: mshick/add-pr-comment@ec328af66588ab8f77cdeb2c264f14aba45bbf59 # v3
         with:
           message: |
             ## This PR is against the `main` branch :x:
diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index 355e3fc9ff..4847d9063d 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -31,7 +31,7 @@ jobs:
           PR_NUMBER="${{ github.event.issue.number }}"
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
@@ -60,12 +60,12 @@ jobs:
           echo "changed=$file_changed" >> $GITHUB_OUTPUT
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
       - name: Run pre-commit rules with prek
-        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
+        uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2
         continue-on-error: true
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 33ab1652b3..a344acff45 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -47,7 +47,7 @@ jobs:
 
       # Set up nf-core/tools
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 47048ba41d..698ee79f53 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -59,7 +59,7 @@ jobs:
         uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 667821f695..e394ddd041 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -45,7 +45,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
index 0e76048c38..f843e0b321 100644
--- a/.github/workflows/deploy-pypi.yml
+++ b/.github/workflows/deploy-pypi.yml
@@ -17,7 +17,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 285c517c4e..f04cfdf678 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@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
+        uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2
         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 37f2e68d44..d7efa84e9b 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -22,6 +22,6 @@ jobs:
       - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
 
       - name: Run prek
-        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
+        uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
diff --git a/.github/workflows/nextflow-source-test.yml b/.github/workflows/nextflow-source-test.yml
index a02fae87db..d53cb46728 100644
--- a/.github/workflows/nextflow-source-test.yml
+++ b/.github/workflows/nextflow-source-test.yml
@@ -20,7 +20,7 @@ jobs:
           path: nextflow
 
       - name: Set up Java
-        uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5
+        uses: actions/setup-java@1bcf9fb12cf4aa7d266a90ae39939e61372fe520 # v5
         with:
           distribution: "temurin"
           architecture: x64
@@ -45,7 +45,7 @@ jobs:
 
       # Set up nf-core/tools
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 1c6009cf00..c31e0dfb43 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -76,7 +76,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: ${{ matrix.python-version }}
           token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 5d4ff98ba0..42a4bbc98b 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -77,7 +77,7 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml
index 910e93785b..11f9f5e915 100644
--- a/.github/workflows/update-template-snapshots.yml
+++ b/.github/workflows/update-template-snapshots.yml
@@ -56,7 +56,7 @@ jobs:
 
       # Install dependencies and run pytest
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml
index bbb7534ab4..e441f4f37c 100644
--- a/.github/workflows/update-textual-snapshots.yml
+++ b/.github/workflows/update-textual-snapshots.yml
@@ -37,7 +37,7 @@ jobs:
 
       # Install dependencies and run pytest
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
 
diff --git a/nf_core/pipeline-template/.github/actions/nf-test/action.yml b/nf_core/pipeline-template/.github/actions/nf-test/action.yml
index 17137be3ab..90397426f6 100644
--- a/nf_core/pipeline-template/.github/actions/nf-test/action.yml
+++ b/nf_core/pipeline-template/.github/actions/nf-test/action.yml
@@ -25,7 +25,7 @@ runs:
         version: "{% raw %}${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
       with:
         python-version: "3.14"
 
diff --git a/nf_core/pipeline-template/.github/workflows/branch.yml b/nf_core/pipeline-template/.github/workflows/branch.yml
index 27468bc072..7677c6f9e5 100644
--- a/nf_core/pipeline-template/.github/workflows/branch.yml
+++ b/nf_core/pipeline-template/.github/workflows/branch.yml
@@ -21,7 +21,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
+        uses: mshick/add-pr-comment@ec328af66588ab8f77cdeb2c264f14aba45bbf59 # v3
         with:
           message: |
             ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index b2dad9611b..9d78212009 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -47,7 +47,7 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
diff --git a/nf_core/pipeline-template/.github/workflows/fix_linting.yml b/nf_core/pipeline-template/.github/workflows/fix_linting.yml
index 17314baca5..1cdbc24762 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@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
+        uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2
         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 05f710dce7..4186ad6982 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@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
       - name: Run prek
-        uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2
+        uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2
 
   nf-core:
     runs-on: ubuntu-latest
@@ -28,7 +28,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
diff --git a/nf_core/pipeline-template/.github/workflows/template-version-comment.yml b/nf_core/pipeline-template/.github/workflows/template-version-comment.yml
index a3333571e1..36ab701eb5 100644
--- a/nf_core/pipeline-template/.github/workflows/template-version-comment.yml
+++ b/nf_core/pipeline-template/.github/workflows/template-version-comment.yml
@@ -29,7 +29,7 @@ jobs:
         run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
-        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
+        uses: mshick/add-pr-comment@ec328af66588ab8f77cdeb2c264f14aba45bbf59 # v3
         if: |
           contains(env.OUTPUT, 'nf-core')
         with: