troubleshooting

cidgoh · Nov 27, 2024 · f65776c · f65776c
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diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
@@ -1,100 +1,106 @@
 name: "nf-test Action"
 description: "Runs nf-test with common setup steps"
 inputs:
-    profile:
-        description: "Profile to use"
-        required: true
-    component_path:
-        description: "Path to the component to test"
-        required: true
-    tags:
-        description: "Tags to test (`<tags>[,<tags>...]`)"
-        required: false
+  profile:
+    description: "Profile to use"
+    required: true
+  component_path:
+    description: "Path to the component to test"
+    required: true
+  tags:
+    description: "Tags to test (`<tags>[,<tags>...]`)"
+    required: false
 
 runs:
-    using: "composite"
-    steps:
-        - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
-          with:
-              distribution: "temurin"
-              java-version: "17"
+  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: "${{ env.NXF_VERSION }}"
+    - name: Setup Nextflow
+      uses: nf-core/setup-nextflow@v2
+      with:
+        version: "${{ env.NXF_VERSION }}"
 
-        - name: Set up Python
-          uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-          with:
-              python-version: "3.11"
+    - name: 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: "${{ env.NFT_VER }}"
-              install-pdiff: true
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: "${{ env.NFT_VER }}"
+        install-pdiff: true
 
-        - name: Setup apptainer
-          if: contains(inputs.profile, 'singularity')
-          uses: eWaterCycle/setup-apptainer@main
+    - 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: 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: 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")
+    - 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")
 
-        - name: Run nf-test
-          shell: bash
-          env:
-              SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
-              SENTIEON_AUTH_MECH: "GitHub Actions - token"
-              TAGS: ${{ inputs.tags && format('--tag {0}', inputs.tags) || '' }}
-              NFT_WORKDIR: "~"
-          run: |
-              cd ${{ inputs.component_path }}
-              if [ ! -f "tests/main.nf.test" ]; then
-                echo "No tests found in ${{ inputs.component_path }}/tests/"
-                echo "No tests executed" > test.tap
-              else
-                nf-test test \
-                  --profile=${{ inputs.profile }} \
-                  --tap=test.tap \
-                  --verbose \
-                  --ci \
-                  --filter process,workflow \
-                  --follow-dependencies \
-                  ${{ env.TAGS }} || true
-              fi
+    - name: Run nf-test
+      shell: bash
+      env:
+        SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
+        SENTIEON_AUTH_MECH: "GitHub Actions - token"
+        TAGS: ${{ inputs.tags && format('--tag {0}', inputs.tags) || '' }}
+        NFT_WORKDIR: "~"
+      run: |
+        cd ${{ inputs.component_path }}
+        echo "Current directory: $(pwd)"
+        echo "Contents of current directory:"
+        ls -la
+        echo "Contents of tests directory (if exists):"
+        ls -la tests || echo "No tests directory found"
 
-              # Display test.tap content for debugging
-              echo "Contents of test.tap:"
-              cat test.tap
+        if [ -d "tests" ] && [ "$(ls -A tests)" ]; then
+          echo "Running nf-test..."
+          nf-test test \
+            --profile=${{ inputs.profile }} \
+            --tap=test.tap \
+            --verbose \
+            --ci \
+            --filter process,workflow \
+            --follow-dependencies \
+            ${{ env.TAGS }} || true
+        else
+          echo "No tests found in ${{ inputs.component_path }}/tests/"
+          echo "No tests executed" > test.tap
+        fi
 
-        - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
-          if: always()
-          with:
-              path: ${{ inputs.component_path }}/test.tap
+        echo "Contents of test.tap:"
+        cat test.tap || echo "test.tap file not found"
 
-        - name: Clean up
-          if: always()
-          shell: bash
-          run: |
-              sudo rm -rf /home/ubuntu/tests/
+    - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
+      if: always()
+      with:
+        path: ${{ inputs.component_path }}/test.tap
+
+    - name: Clean up
+      if: always()
+      shell: bash
+      run: |
+        sudo rm -rf /home/ubuntu/tests/
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -40,7 +40,7 @@ jobs:
         id: get-components
         run: |
           components=$(find modules/nf-core subworkflows/nf-core -type d -maxdepth 2 -mindepth 1 | while read component; do
-            if [ -d "$component/tests" ]; then
+            if [ -d "$component/tests" ] && [ "$(ls -A $component/tests)" ]; then
               echo "$component"
             fi
           done | jq -R -s -c 'split("\n") | map(select(length > 0))')
@@ -84,3 +84,11 @@ jobs:
         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: 1