nf-core · mashehu · Jul 23, 2026 · Jul 23, 2026
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -11,54 +11,50 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
-      - name: Set up Python 3.14
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files
+      - name: Run prek
+        uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
 
+      - name: Setup uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+        run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' }}
+        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
-        if: ${{ github.base_ref == 'master' }}
+        if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -71,7 +67,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: linting-logs
           path: |

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.3"
+  NFT_VER: "0.9.4"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           fetch-depth: 0
 
@@ -78,14 +78,14 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
+          - "25.10.4"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           fetch-depth: 0
 
@@ -116,6 +116,22 @@ jobs:
             fi
           fi
 
+      # continue-on-error keeps latest-everything from failing the job, so it never shows up in
+      # `needs.nf-test.result` downstream and CI stays green. Surface it via a PR comment instead;
+      # other NXF_VER failures already fail the job/CI directly, so no comment is needed for those.
+      - name: Prepare PR comment fragment
+        if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }}
+        run: |
+          mkdir -p pr-comment-fragment
+          echo "* ❌ \`${{ matrix.profile }}\` | \`${{ matrix.NXF_VER }}\` | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" > pr-comment-fragment/fragment.md
+
+      - name: Upload PR comment fragment
+        if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }}
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-comment-fragment-${{ strategy.job-index }}
+          path: pr-comment-fragment/
+
   confirm-pass:
     needs: [nf-test]
     if: always()
@@ -142,3 +158,42 @@ jobs:
           echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
           echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
           echo "::endgroup::"
+
+      - name: Download PR comment fragments
+        if: ${{ always() }}
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        continue-on-error: true
+        with:
+          pattern: pr-comment-fragment-*
+          path: pr-comment-fragments
+          merge-multiple: true
+
+      # Build a comment for the shared pr-comment.yml poster to publish on the PR.
+      # Based on the fragments above (not needs.*.result) so non-blocking failures are still reported.
+      - name: Prepare PR comment
+        if: ${{ always() }}
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+        run: |
+          mkdir -p pr-comment
+          echo "$PR_NUMBER" > pr-comment/pr_number.txt
+          echo "nf-test" > pr-comment/header.txt
+          if [ -d pr-comment-fragments ] && [ -n "$(ls -A pr-comment-fragments)" ]; then
+            {
+              echo "## ❌ nf-test failed"
+              echo ""
+              echo "> [!NOTE]:"
+              echo "> Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected with newer (edge-)releases of Nextflow or if it needs fixing."
+              cat pr-comment-fragments/*.md
+              echo ""
+              echo "See the [full run](${RUN_URL}) for details."
+            } > pr-comment/comment.md
+          fi
+
+      - name: Upload PR comment artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-comment
+          path: pr-comment/
diff --git a/.github/workflows/pr-comment.yml b/.github/workflows/pr-comment.yml
@@ -18,6 +18,7 @@ on:
       - "nf-core linting"
       - "nf-core template version comment"
       - "nf-core branch protection"
+      - "Run nf-test"
 
 permissions:
   actions: read