troubleshooting

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

@@ -17,18 +17,18 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+    - uses: actions/setup-java@v4
       with:
         distribution: "temurin"
         java-version: "17"
 
     - name: Setup Nextflow
       uses: nf-core/setup-nextflow@v2
       with:
-        version: "${{ env.NXF_VERSION }}"
+        version: "${{ env.NXF_VER }}"
 
     - name: Set up Python
-      uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      uses: actions/setup-python@v5
       with:
         python-version: "3.11"
 
@@ -51,22 +51,19 @@ runs:
 
     - name: Conda setup
       if: ${{inputs.profile == 'conda'}}
-      uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
+      uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         conda-solver: libmamba
         conda-remove-defaults: true
 
-    # Set up secrets
     - 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")
 
-      # TODO Skip failing conda tests and document their failures
-      # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
       shell: bash
       env:
@@ -85,12 +82,9 @@ runs:
           --follow-dependencies \
           ${{ env.TAGS }}
 
-      # TODO If no test.tap, then make one to spoof?
-    - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
-      if: ${{ inputs.path != '' }}
+    - uses: pcolby/tap-summary@v1
       with:
-        path: >-
-          test.tap
+        path: test.tap
 
     - name: Clean up
       if: always()