troubleshooting

.github/actions/nf-test-action/action.yml

@@ -14,7 +14,58 @@ inputs:
 runs:
   using: "composite"
   steps:
-    # ... (keep all the setup steps as they are)
+    - 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
+
+    - 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")
 
     - name: Run nf-test
       shell: bash

.github/workflows/ci.yml

@@ -87,4 +87,4 @@ jobs:
         with:
           name: nf-test-results-${{ matrix.component }}-${{ matrix.profile }}
           path: ${{ matrix.component }}/test.tap
-          retention-days: 1
+          retention-days: 5