nf-core · mashehu · Jun 30, 2025 · Apr 24, 2025 · Apr 24, 2025 · Apr 24, 2025
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
@@ -31,8 +31,6 @@ jobs:
     outputs:
       all_features: ${{ steps.create_matrix.outputs.matrix }}
     steps:
-      - name: 🏗 Set up yq
-        uses: frenck/action-setup-yq@c4b5be8b4a215c536a41d436757d9feb92836d4f # v1
       - name: checkout
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - name: Create Matrix

diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml
@@ -92,13 +92,31 @@ jobs:
           fetch-depth: 0
 
       - name: Run nf-test
+        id: run_nf_test
         uses: ./.github/actions/nf-test
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
           total_shards: ${{ env.TOTAL_SHARDS }}
+
+      - name: Report test status
+        if: ${{ always() }}
+        run: |
+          if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then
+            echo "::error::Test with ${{ matrix.NXF_VER }} failed"
+            # Add to workflow summary
+            echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY
+            if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then
+              echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing."
+            fi
+            if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+              exit 1
+            fi
+          fi
+
   confirm-pass:
     needs: [nf-test]
     if: always()
@@ -107,7 +125,7 @@ jobs:
       - runner=2cpu-linux-x64{% else %} use GitHub runners
       - "ubuntu-latest"{% endif %}{% raw %}
     steps:
-      - name: One or more tests failed
+      - name: One or more tests failed (excluding latest-everything)
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
@@ -125,12 +143,4 @@ jobs:
           echo "::group::DEBUG: `needs` Contents"
           echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
           echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
-          echo "::endgroup::"
-
-      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
-        if: always()
-        run: |
-          ls -la ./
-          rm -rf ./* || true
-          rm -rf ./.??* || true
-          ls -la ./{% endraw %}
+          echo "::endgroup::"{% endraw %}