Important! Template update for nf-core/tools v3.3.2

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

@@ -54,13 +54,9 @@ runs:
         conda-solver: libmamba
         conda-remove-defaults: true
 
-      # TODO Skip failing conda tests and document their failures
-      # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
       shell: bash
       env:
-        NFT_DIFF: ${{ env.NFT_DIFF }}
-        NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
         NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
       run: |
         nf-test test \

.github/workflows/linting.yml

@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
           python-version: "3.13"

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10
+        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.github/workflows/nf-test.yml

@@ -1,16 +1,5 @@
 name: Run nf-test
 on:
-  push:
-    branches:
-      - dev
-      - master
-      - main
-    paths-ignore:
-      - "docs/**"
-      - "**/meta.yml"
-      - "**/*.md"
-      - "**/*.png"
-      - "**/*.svg"
   pull_request:
     paths-ignore:
       - "docs/**"
@@ -39,8 +28,9 @@ jobs:
   nf-test-changes:
     name: nf-test-changes
     runs-on: # use self-hosted runners
-      - runs-on=$-nf-test-changes
+      - runs-on=${{ github.run_id }}-nf-test-changes
       - runner=4cpu-linux-x64
+      - disk=large
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
       total_shards: ${{ steps.set-shards.outputs.total_shards }}
@@ -74,7 +64,7 @@ jobs:
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
     runs-on: # use self-hosted runners
-      - runs-on=$-nf-test
+      - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
       - disk=large
     strategy:
@@ -91,7 +81,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.04.2"
+          - "24.10.5"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
@@ -103,138 +93,39 @@ 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 }}
-          tags: modules_local,subworkflows_local
-
-  pipeline-tests:
-    name: "Pipeline Test | ${{ matrix.test_name }} | ${{ matrix.NXF_VER }} | ${{ matrix.profile }}"
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        test_name:
-          - "default"
-          - "main_pipeline_build"
-          - "main_pipeline_extend"
-          - "main_pipeline_sub"
-          - "main_pipeline_qc"
-          - "main_pipeline_reference_mapping"
-        profile: [conda, docker, singularity]
-        isMain:
-          - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
-        # Exclude conda and singularity on dev
-        exclude:
-          - isMain: false
-            profile: "conda"
-          - isMain: false
-            profile: "singularity"
-        NXF_VER:
-          - "24.04.2"
-          - "latest-everything"
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-        with:
-          fetch-depth: 0
-
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Set up Python
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
-        with:
-          python-version: "3.13"
-
-      - name: Install nf-test
-        uses: nf-core/setup-nf-test@v1
-        with:
-          version: ${{ env.NFT_VER }}
-          install-pdiff: true
-
-      - name: Setup apptainer
-        if: contains(matrix.profile, 'singularity')
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: contains(matrix.profile, 'singularity')
-        shell: bash
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Conda setup
-        if: contains(matrix.profile, 'conda')
-        uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
-        with:
-          auto-update-conda: true
-          conda-solver: libmamba
-          conda-remove-defaults: true
-
-      - name: Run nf-test
-        shell: bash
-        env:
-          NFT_DIFF: ${{ env.NFT_DIFF }}
-          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
-          NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+      - name: Report test status
+        if: ${{ always() }}
         run: |
-          # Make it clear that we're ONLY running tests from the tests directory
-          # and not including any module or subworkflow tests
-          nf-test test \
-            --profile=+${{ matrix.profile }} \
-            --ci \
-            --verbose \
-            --tap=test.tap \
-            tests/${{ matrix.test_name }}.nf.test
-
-      - name: Generate test summary
-        if: always()
-        shell: bash
-        run: |
-          # Add header if it doesn't exist (using a token file to track this)
-          if [ ! -f ".summary_header" ]; then
-            echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
-            echo "" >> $GITHUB_STEP_SUMMARY
-            echo "| Status | Test Name | Profile | Nextflow Version |" >> $GITHUB_STEP_SUMMARY
-            echo "|:------:|-----------|---------|-----------------|" >> $GITHUB_STEP_SUMMARY
-            touch .summary_header
-          fi
-
-          if [ -f test.tap ]; then
-            while IFS= read -r line; do
-              if [[ $line =~ ^ok ]]; then
-                test_name="${line#ok }"
-                # Remove the test number from the beginning
-                test_name="${test_name#* }"
-                echo "| ✅ | ${test_name} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} |" >> $GITHUB_STEP_SUMMARY
-              elif [[ $line =~ ^not\ ok ]]; then
-                test_name="${line#not ok }"
-                # Remove the test number from the beginning
-                test_name="${test_name#* }"
-                echo "| ❌ | ${test_name} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} |" >> $GITHUB_STEP_SUMMARY
-              fi
-            done < test.tap
-          else
-            echo "| ⚠️ | No test results found | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} |" >> $GITHUB_STEP_SUMMARY
+          if [[ "${{ 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, pipeline-tests]
     if: always()
     runs-on: # use self-hosted runners
-      - runs-on=$-confirm-pass
+      - runs-on=${{ github.run_id }}-confirm-pass
       - runner=2cpu-linux-x64
     steps:
-      - name: One or more tests failed
+      - name: One or more tests failed (excluding latest-everything)
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
@@ -253,11 +144,3 @@ jobs:
           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 ./

.github/workflows/release-announcements.yml

@@ -30,7 +30,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0
+      - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!

.nf-core.yml

@@ -1,4 +1,4 @@
-nf_core_version: 3.3.1
+nf_core_version: 3.3.2
 repository_type: pipeline
 template:
   author: Nico Trummer

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.5.0
+          - prettier@3.6.2
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:

README.md

@@ -5,14 +5,12 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/scdownstream/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/scdownstream/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/scdownstream/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/scdownstream/actions/workflows/linting.yml)
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/scdownstream/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions CI Status](https://github.com/nf-core/scdownstream/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/scdownstream/actions/workflows/nf-test.yml)
+[![GitHub Actions Linting Status](https://github.com/nf-core/scdownstream/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/scdownstream/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/scdownstream/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

modules.json

@@ -32,7 +32,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
+                        "git_sha": "c9a31c472ef2d86802eb44f27322955849859361",
                         "installed_by": ["modules"]
                     },
                     "scvitools/scar": {