Update GitHub Actions

.github/workflows/changelog.yml

@@ -36,7 +36,7 @@ jobs:
           fi
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 
@@ -65,7 +65,7 @@ jobs:
           echo "File changed: ${{ env.changed }}"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
           cache: "pip"

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

@@ -53,7 +53,7 @@ jobs:
 
       # Set up nf-core/tools
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
           cache: pip

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

@@ -65,7 +65,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 

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

@@ -52,7 +52,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 

.github/workflows/deploy-pypi.yml

@@ -17,7 +17,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 

.github/workflows/fix-linting.yml

@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 

.github/workflows/lint-code.yml

@@ -21,7 +21,7 @@ jobs:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
           cache: "pip"

.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@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
@@ -160,7 +160,7 @@ jobs:
 
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
@@ -184,7 +184,7 @@ jobs:
           coverage report
           coverage xml
 
-      - uses: codecov/codecov-action@54bcd8715eee62d40e33596ef5e8f0f48dbbccab # v4
+      - uses: codecov/codecov-action@c16abc29c95fcf9174b58eb7e1abf4c866893bc8 # v4
         with:
           files: coverage.xml
         env:

.github/workflows/rich-codex.yml

@@ -8,7 +8,7 @@ jobs:
       - name: Check out the repo
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
       - name: Set up Python
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: 3.x
           cache: pip

.github/workflows/sync.yml

@@ -57,7 +57,7 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 

.github/workflows/update_components_template.yml

@@ -14,7 +14,7 @@ jobs:
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Set up Python
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.x"
 

CHANGELOG.md

@@ -44,6 +44,7 @@
 - Make cli-provided module/subworkflow names case insensitive ([#2869](https://github.com/nf-core/tools/pull/2869))
 - Update gitpod/workspace-base Docker digest to 168d78b ([#2899](https://github.com/nf-core/tools/pull/2899))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.3.4 ([#2894](https://github.com/nf-core/tools/pull/2894))
+- Update GitHub Actions ([#2902](https://github.com/nf-core/tools/pull/2902))
 
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]
 

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

@@ -35,7 +35,7 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
           architecture: "x64"

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

@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 

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

@@ -17,7 +17,7 @@ jobs:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
           cache: "pip"
@@ -37,7 +37,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
           architecture: "x64"

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

@@ -31,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies