chore(deps): bump the github-actions group across 1 directory with 10 updates

.github/workflows/auto-format.yml

@@ -16,16 +16,16 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
           ref: ${{ github.event_name == 'pull_request' && github.head_ref || github.ref_name }}
 
-      - uses: actions/setup-python@v6
+      - uses: actions/setup-python@v7
         with:
           python-version: 3.14
       - name: Install nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@v3
       - name: git config
         run: |
           git config --global user.name "github-actions[bot]"

.github/workflows/build-nextflow.yml

@@ -35,17 +35,17 @@ jobs:
       matrix:
         python-version: ["3.14"]
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
           ref: ${{ github.event_name == 'pull_request' && github.head_ref || github.ref_name }}
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v7
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
       - name: Install nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v3
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip setuptools
@@ -64,7 +64,7 @@ jobs:
           tool_name run -c conf/ci_stub.config -stub --mode local
           popd
       - name: "Upload Artifact"
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         if: always() # run even if previous steps fail
         with:
           name: nextflow-log
@@ -77,12 +77,12 @@ jobs:
       nf_test_files: ${{ steps.list.outputs.components }}
     if: ${{ github.event_name == 'pull_request' }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - name: List nf-test files
         id: list
-        uses: adamrtalbot/detect-nf-test-changes@v0.0.6
+        uses: adamrtalbot/detect-nf-test-changes@accef9459c66baa65dbca647615f088b98eefa9c
         with:
           head: ${{ github.sha }}
           base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha || 'origin/master' }}
@@ -116,9 +116,9 @@ jobs:
             profile: "singularity"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v4
       - name: Set up Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@v3
         with:
           version: "${{ matrix.NXF_VER }}"
       - name: Set up Apptainer
@@ -130,10 +130,10 @@ jobs:
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
       - name: Install nf-test
-        uses: nf-core/setup-nf-test@v1
+        uses: nf-core/setup-nf-test@v2
         with:
           version: ${{ env.NFT_VER }}
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v7
         with:
           python-version: "3.14"
           architecture: "x64"
@@ -142,7 +142,7 @@ jobs:
           python -m pip install --upgrade pip
           pip install pdiff
       - name: Clean up Disk space
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+        uses: jlumbroso/free-disk-space@ceedf095f4ec1a097402bc6bd80831f2e1a6fde6 # v2.0.0
 
       - name: Run nf-test
         run: |
@@ -158,7 +158,7 @@ jobs:
           sudo apt install bat > /dev/null
           batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
       - name: Publish Test Report
-        uses: mikepenz/action-junit-report@v3
+        uses: mikepenz/action-junit-report@v6
         if: always() # always run even if the previous step fails
         with:
           report_paths: test.xml

.github/workflows/docs-mkdocs.yml

@@ -19,9 +19,9 @@ jobs:
   mkdocs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
-      - uses: CCBR/actions/mkdocs-mike@v0.5
+      - uses: CCBR/actions/mkdocs-mike@v0.7
         with:
           github-token: ${{ github.token }}

.github/workflows/draft-release.yml

@@ -17,10 +17,10 @@ jobs:
   draft-release:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0 # required to include tags
-      - uses: CCBR/actions/draft-release@v0.5
+      - uses: CCBR/actions/draft-release@v0.7
         with:
           github-token: ${{ github.token }}
           version-tag: ${{ github.event.inputs.version-tag }}

.github/workflows/post-release.yml

@@ -14,9 +14,9 @@ jobs:
   cleanup:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
-      - uses: CCBR/actions/post-release@v0.5
+      - uses: CCBR/actions/post-release@v0.7
         with:
           github-token: ${{ github.token }}

.github/workflows/techdev-project.yml

@@ -20,13 +20,13 @@ jobs:
       - name: Generate a token
         id: generate-token
         if: ${{ inputs.github-token == '' }}
-        uses: actions/create-github-app-token@v2
+        uses: actions/create-github-app-token@v3
         with:
-          app-id: ${{ vars.CCBR_BOT_APP_ID }}
+          client-id: ${{ vars.CCBR_BOT_CLIENT_ID }}
           private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
           owner: CCBR
 
-      - uses: actions/add-to-project@v1.0.2
+      - uses: actions/add-to-project@v2.0.0
         with:
           project-url: https://github.com/orgs/CCBR/projects/17
           github-token: ${{ steps.generate-token.outputs.token }}

.github/workflows/user-projects.yml

@@ -16,8 +16,8 @@ jobs:
   add-to-project:
     runs-on: ubuntu-latest
     steps:
-      - uses: CCBR/actions/user-projects@v0.5
+      - uses: CCBR/actions/user-projects@v0.7
         with:
-          app-id: ${{ vars.CCBR_BOT_APP_ID }}
+          client-id: ${{ vars.CCBR_BOT_CLIENT_ID }}
           app-private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
           token-owner: "CCBR"