troubleshooting

cidgoh · Nov 27, 2024 · aaa217d · aaa217d
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diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
@@ -14,58 +14,13 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
-      with:
-        distribution: "temurin"
-        java-version: "17"
-
-    - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@v2
-      with:
-        version: "${{ env.NXF_VERSION }}"
-
-    - name: Set up Python
-      uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-      with:
-        python-version: "3.11"
-
-    - name: Install nf-test
-      uses: nf-core/setup-nf-test@v1
-      with:
-        version: "${{ env.NFT_VER }}"
-        install-pdiff: true
+    # ... (keep all the setup steps as they are)
 
     - name: Verify nf-test installation
       shell: bash
       run: |
-        which nf-test || echo "nf-test not found in PATH"
-        nf-test --version || echo "nf-test command failed"
-
-    - name: Setup apptainer
-      if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@main
-
-    - name: Set up Singularity
-      if: contains(inputs.profile, 'singularity')
-      shell: bash
-      run: |
-        mkdir -p $NXF_SINGULARITY_CACHEDIR
-        mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-    - name: Conda setup
-      if: ${{inputs.profile == 'conda'}}
-      uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
-      with:
-        auto-update-conda: true
-        conda-solver: libmamba
-        conda-remove-defaults: true
-
-    - name: Set up nextflow secrets
-      if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != ''
-      shell: bash
-      run: |
-        python -m pip install cryptography
-        nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+        which nf-test
+        nf-test version
 
     - name: Run nf-test
       shell: bash

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -75,8 +75,40 @@ jobs:
         with:
           fetch-depth: 1
 
+      - name: Setup Java
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: '17'
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: ${{ env.NXF_VER }}
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFT_VER }}
+
+      - name: Print nf-test version
+        run: nf-test version
+
       - name: Run nf-test Action
         uses: ./.github/actions/nf-test-action
         with:
           profile: ${{ matrix.profile }}
           component_path: ${{ matrix.component }}
+
+      - name: Upload test results
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          name: nf-test-results-${{ matrix.component }}-${{ matrix.profile }}
+          path: ${{ matrix.component }}/test.tap
+          retention-days: 5