chore(deps): update github actions

.github/actions/create-lint-wf/action.yml

@@ -88,7 +88,7 @@ runs:
 
     - name: Upload log file artifact
       if: ${{ always() }}
-      uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+      uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4
       with:
         name: nf-core-log-file-${{ matrix.NXF_VER }}
         path: create-lint-wf/log.txt

.github/workflows/changelog.yml

@@ -36,9 +36,9 @@ jobs:
           fi
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install packages
         run: |
@@ -65,9 +65,9 @@ jobs:
           echo "File changed: ${{ env.changed }}"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           cache: "pip"
 
       - name: Install pre-commit

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
+      - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."

.github/workflows/create-lint-wf.yml

@@ -51,9 +51,9 @@ jobs:
 
       # Set up nf-core/tools
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           cache: pip
 
       - name: Install python dependencies

.github/workflows/create-test-lint-wf-template.yml

@@ -38,7 +38,7 @@ jobs:
       all_features: ${{ steps.create_matrix.outputs.matrix }}
     steps:
       - name: 🏗 Set up yq
-        uses: frenck/action-setup-yq@v1
+        uses: frenck/action-setup-yq@c4b5be8b4a215c536a41d436757d9feb92836d4f # v1
       - name: checkout
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - name: Create Matrix
@@ -82,9 +82,9 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install python dependencies
         run: |
@@ -180,7 +180,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4
         with:
           name: nf-core-log-file-${{ matrix.TEMPLATE }}
           path: create-test-lint-wf/artifact_files.tar

.github/workflows/create-test-wf.yml

@@ -50,9 +50,9 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install python dependencies
         run: |
@@ -73,7 +73,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4
         with:
           name: nf-core-log-file-${{ matrix.NXF_VER }}
           path: create-test-wf/log.txt

.github/workflows/deploy-pypi.yml

@@ -17,9 +17,9 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install python dependencies
         run: |

.github/workflows/fix-linting.yml

@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit

.github/workflows/lint-code.yml

@@ -21,9 +21,9 @@ jobs:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           cache: "pip"
 
       - name: Install pre-commit

.github/workflows/pytest.yml

@@ -91,7 +91,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
@@ -148,15 +148,15 @@ jobs:
           echo "test=${test}" >> $GITHUB_ENV
 
       - name: Store snapshot report
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4
         if: always()
         with:
           include-hidden-files: true
           name: Snapshot Report ${{ env.test }}
           path: ./snapshot_report.html
 
       - name: Upload coverage
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4
         with:
           include-hidden-files: true
           name: coverage_${{ env.test }}
@@ -174,11 +174,11 @@ jobs:
 
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           cache: "pip"
 
       - name: Install dependencies
@@ -191,14 +191,14 @@ jobs:
           mv .github/.coveragerc .
 
       - name: Download all artifacts
-        uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
+        uses: actions/download-artifact@cc203385981b70ca67e1cc392babf9cc229d5806 # v4
       - name: Run coverage
         run: |
           coverage combine --keep coverage*/.coverage*
           coverage report
           coverage xml
 
-      - uses: codecov/codecov-action@5c47607acb93fed5485fdbf7232e8a31425f672a # v5
+      - uses: codecov/codecov-action@0565863a31f2c772f9f0395002a31e3f06189574 # v5
         with:
           files: coverage.xml
         env:

.github/workflows/sync.yml

@@ -79,9 +79,9 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install python dependencies
         run: |
@@ -123,7 +123,7 @@ jobs:
 
       - name: Upload sync log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4
         with:
           name: sync_log_${{ matrix.pipeline }}
           path: sync_log_${{ matrix.pipeline }}.txt

.github/workflows/update-textual-snapshots.yml

@@ -33,9 +33,9 @@ jobs:
 
       # Install dependencies and run pytest
       - name: Set up Python
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           cache: "pip"
 
       - name: Install dependencies

CHANGELOG.md

@@ -40,6 +40,7 @@
 - chore(deps): update gitpod/workspace-base docker digest to 7f35e40 ([#3473](https://github.com/nf-core/tools/pull/3473))
 - chore(deps): update python:3.12-slim docker digest to aaa3f8c ([#3474](https://github.com/nf-core/tools/pull/3474))
 - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.9 ([#3470](https://github.com/nf-core/tools/pull/3470))
+- chore(deps): update github actions ([#3488](https://github.com/nf-core/tools/pull/3488))
 
 ## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]
 

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

@@ -61,7 +61,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4
         with:
           name: Seqera Platform debug log file
           path: |

nf_core/pipeline-template/.github/workflows/awstest.yml

@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4
         with:
           name: Seqera Platform debug log file
           path: |

nf_core/pipeline-template/.github/workflows/ci.yml

@@ -61,7 +61,7 @@ jobs:
 
       - name: Set up Miniconda
         if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
         with:
           miniconda-version: "latest"
           auto-update-conda: true

nf_core/pipeline-template/.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
+      - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."

nf_core/pipeline-template/.github/workflows/download_pipeline.yml

@@ -44,9 +44,9 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: Setup Apptainer
@@ -127,7 +127,7 @@ jobs:
           fi{% endraw %}
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*

nf_core/pipeline-template/.github/workflows/fix-linting.yml

@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit

nf_core/pipeline-template/.github/workflows/linting.yml

@@ -14,9 +14,9 @@ jobs:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -33,13 +33,13 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/[email protected]
+        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4
         with:
           name: linting-logs
           path: |

nf_core/pipeline-template/.github/workflows/linting_comment.yml

@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
+        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

nf_core/pipeline-template/.github/workflows/release-announcements.yml

@@ -30,7 +30,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0
+      - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!

nf_core/pipeline-template/.github/workflows/template_version_comment.yml

@@ -14,7 +14,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: nichmor/[email protected]
+        uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml