testing include-hidden-files

bigbio · Oct 7, 2024 · 87e2129 · 87e2129
1 parent 1dc3e6d
commit 87e2129
Showing 1 changed file with 6 additions and 3 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -84,7 +84,7 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow -log pipeline.log run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
+          nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
 
       - name: Run pipeline with test data in conda profile (and single-threaded)
         env:
@@ -94,7 +94,7 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow -log pipeline.log run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,micromamba --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
+          nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,micromamba --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
 
       - name: Gather failed logs
         if: failure() || cancelled()
@@ -104,6 +104,7 @@ jobs:
           while read -r line ; do cp $(ls work/${line}*/*.log) failed_logs/ | true ; done <<< "$failed"
 
       - uses: actions/upload-artifact@v4
+        include-hidden-files: true
         if: failure() || cancelled()
         name: Upload failed logs
         with:
@@ -112,6 +113,7 @@ jobs:
           overwrite: false
 
       - uses: actions/upload-artifact@v4
+        include-hidden-files: true
         if: always()
         name: Upload results
         with:
@@ -120,9 +122,10 @@ jobs:
           overwrite: false
 
       - uses: actions/upload-artifact@v4
+        include-hidden-files: true
         if: always()
         name: Upload log
         with:
           name: nextflow_${{ matrix.test_profile }}_${{ matrix.exec_profile }}_${{ matrix.NXF_VER }}.log
-          path: pipeline.log
+          path: .nextflow.log
           overwrite: false