ci: Bump the github-actions group across 1 directory with 19 updates

.github/workflows/build.yml

@@ -28,7 +28,7 @@ jobs:
         os: [ubuntu-latest, macos-latest]
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
         with:
           persist-credentials: false
 
@@ -62,15 +62,15 @@ jobs:
         uses: dtolnay/rust-toolchain@4be9e76fd7c4901c61fb841f559994984270fce7  # stable
 
       - name: Set up sccache
-        uses: mozilla-actions/sccache-action@7d986dd989559c6ecdb630a3fd2557667be217ad  # v0.0.9
+        uses: mozilla-actions/sccache-action@fc920bf0ec8de6ee65d409111f7ec508035751ba  # v0.0.11
 
       - name: Configure sccache
         run: |
           echo "SCCACHE_GHA_ENABLED=true" >> $GITHUB_ENV
           echo "RUSTC_WRAPPER=sccache" >> $GITHUB_ENV
 
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405  # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97  # v6
         with:
           python-version: "3.11"
 
@@ -95,7 +95,7 @@ jobs:
           /tmp/wasp2-wheel/bin/wasp2-count count-cohort --help
 
       - name: Upload wheel artifact
-        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f  # v6
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
         with:
           name: wheel-${{ matrix.os }}
           path: dist/*.whl

.github/workflows/ci.yml

@@ -27,12 +27,12 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
         with:
           persist-credentials: false
 
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405  # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97  # v6
         with:
           python-version: "3.12"
 
@@ -63,7 +63,7 @@ jobs:
       matrix:
         python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
         with:
           persist-credentials: false
 
@@ -83,15 +83,15 @@ jobs:
             bedtools
 
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405  # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97  # v6
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Set up Rust toolchain
         uses: dtolnay/rust-toolchain@4be9e76fd7c4901c61fb841f559994984270fce7  # stable
 
       - name: Set up sccache
-        uses: mozilla-actions/sccache-action@7d986dd989559c6ecdb630a3fd2557667be217ad  # v0.0.9
+        uses: mozilla-actions/sccache-action@fc920bf0ec8de6ee65d409111f7ec508035751ba  # v0.0.11
 
       - name: Configure sccache
         run: |
@@ -130,7 +130,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 20
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
         with:
           persist-credentials: false
 
@@ -152,7 +152,7 @@ jobs:
           components: clippy
 
       - name: Set up sccache
-        uses: mozilla-actions/sccache-action@7d986dd989559c6ecdb630a3fd2557667be217ad  # v0.0.9
+        uses: mozilla-actions/sccache-action@fc920bf0ec8de6ee65d409111f7ec508035751ba  # v0.0.11
 
       - name: Configure sccache
         run: |

.github/workflows/codeql.yml

@@ -32,7 +32,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
         with:
           persist-credentials: false
 

.github/workflows/docker.yml

@@ -26,13 +26,13 @@ jobs:
       matrix:
         platform: [linux/amd64, linux/arm64]
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
         with:
           persist-credentials: false
-      - uses: docker/setup-qemu-action@29109295f81e9208d7d86ff1c6c12d2833863392  # v3
-      - uses: docker/setup-buildx-action@8d2750c68a42422c14e847fe6c8ac0403b4cbd6f  # v3
+      - uses: docker/setup-qemu-action@96fe6ef7f33517b61c61be40b68a1882f3264fb8  # v3
+      - uses: docker/setup-buildx-action@37fe631027851001ddb9b187196cc803df7f5f0e  # v4.3.0
       - name: Build local test image
-        uses: docker/build-push-action@10e90e3645eae34f1e60eeb005ba3a3d33f178e8  # v6
+        uses: docker/build-push-action@53b7df96c91f9c12dcc8a07bcb9ccacbed38856a  # v7.3.0
         with:
           context: .
           load: true

.github/workflows/docs.yml

@@ -20,17 +20,17 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
         with:
           persist-credentials: false
 
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405  # v6
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97  # v6
         with:
           python-version: "3.11"
 
       - name: Cache pip dependencies
-        uses: actions/cache@cdf6c1fa76f9f475f3d7449005a359c84ca0f306  # v5.0.3
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9  # v6.1.0
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-docs-${{ hashFiles('pyproject.toml') }}
@@ -70,7 +70,7 @@ jobs:
 
       - name: Upload artifact
         if: github.ref == 'refs/heads/master' && github.event_name != 'pull_request'
-        uses: actions/upload-pages-artifact@7b1f4a764d45c48632c6b24a0339c27f5614fb0b  # v4
+        uses: actions/upload-pages-artifact@fc324d3547104276b827a68afc52ff2a11cc49c9  # v5.0.0
         with:
           path: docs/build/html
 
@@ -89,4 +89,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e  # v4
+        uses: actions/deploy-pages@cd2ce8fcbc39b97be8ca5fce6e763baed58fa128  # v5.0.0

.github/workflows/ecosystem.yml

@@ -20,10 +20,10 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 45
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
         with:
           persist-credentials: false
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405  # v6
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97  # v6
         with:
           python-version: "3.12"
       - uses: dtolnay/rust-toolchain@4be9e76fd7c4901c61fb841f559994984270fce7  # stable
@@ -46,7 +46,7 @@ jobs:
           planemo test galaxy/tools/wasp2 --no_dependency_resolution --test_output_json galaxy-test-results.json
       - name: Upload Galaxy results
         if: always()
-        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f  # v6
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
         with:
           name: galaxy-test-results
           path: galaxy-test-results.json
@@ -64,20 +64,20 @@ jobs:
       run:
         working-directory: pipelines/${{ matrix.pipeline }}
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
         with:
           persist-credentials: false
-      - uses: nf-core/setup-nextflow@6c2e22b4d901f0c42ca66c5069f8026df026d165  # v2
+      - uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914  # v3.0.1
         with:
           version: "24.10.4"
-      - uses: nf-core/setup-nf-test@f2db585128ae681918440f6c074dededeceadce1  # v1
+      - uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f  # v2.1.0
         with:
           version: "0.9.2"
       - name: Run pipeline compatibility test
         run: nf-test test tests/main.nf.test --tag ci_stub --profile=test_stub --ci --tap=ci-stub.tap --verbose
       - name: Upload nf-test result
         if: always()
-        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f  # v6
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
         with:
           name: nf-test-${{ matrix.pipeline }}
           path: pipelines/${{ matrix.pipeline }}/ci-stub.tap