CI: add gpu tag test job

.github/workflows/ci.yml

@@ -23,8 +23,119 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  test:
-    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
+  nf-test-changes:
+    name: nf-test-changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose detected tags as 'modules' and 'workflows' output variables
+      paths: ${{ steps.list.outputs.components }}
+      modules: ${{ steps.outputs.outputs.modules }}
+      subworkflows: ${{ steps.outputs.outputs.subworkflows}}
+      # Prod for version bumping
+    steps:
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: List nf-test files
+        id: list
+        run: |
+          COMPONENTS=$(nf-test list --tags | grep gpu)
+          echo "components=$COMPONENTS" >> $GITHUB_ENV
+        env:
+          components: ${{ steps.list.outputs.components }}
+
+  nf-test-gpu:
+    runs-on: "gpu"
+    name: "GPU | ${{ matrix.profile }} | ${{ matrix.shard }}"
+    needs: nf-test-changes
+    if: ${{ needs.nf-test-changes.outputs.components != '[]' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        NXF_VER:
+          - "24.04.2"
+          - "latest-everything"
+        shard: [1, 2]
+        filter: [pipeline, workflow]
+        profile:
+          - "docker"
+          - "singularity"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
+    env:
+      NXF_ANSI_LOG: false
+      TOTAL_SHARDS: 2
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Install pdiff to see diff between nf-test snapshots
+        run: |
+          python -m pip install --upgrade pip
+          pip install pdiff
+
+      - uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFT_VER }}
+
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - name: Run GPU Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
+        run: |
+          nf-test test \
+              --ci \
+              --shard ${{ matrix.shard }}/${{ strategy.job-total }} \
+              --changed-since HEAD^ \
+              --profile "+${{ matrix.profile }}" \
+              --filter ${{ matrix.filter }} \
+              --tag "gpu"
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml
+
+  nf-test:
+    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}"
     runs-on: ubuntu-latest
@@ -37,10 +148,9 @@ jobs:
         shard: [1, 2, 3, 4, 5]
         filter: [pipeline, workflow]
         profile:
+          - "conda"
           - "docker"
           - "singularity"
-        test_name:
-          - "test"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev
@@ -106,17 +216,6 @@ jobs:
               --profile "+${{ matrix.profile }}" \
               --filter ${{ matrix.filter }}
 
-      - name: Run GPU Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
-        if: matrix.profile == 'docker' || matrix.profile == 'singularity'
-        run: |
-          nf-test test \
-              --ci \
-              --shard ${{ matrix.shard }}/${{ strategy.job-total }} \
-              --changed-since HEAD^ \
-              --profile "+${{ matrix.profile }}" \
-              --filter ${{ matrix.filter }} \
-              --tag "gpu"
-
       - name: Output log on failure
         if: failure()
         run: |