implement sharding of tests

.github/workflows/ci.yml

@@ -19,75 +19,33 @@ concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 jobs:
-  nf-test-changes:
-    name: Check for changes
-    runs-on: ubuntu-latest
-    outputs:
-      nf_test_files: ${{ steps.list.outputs.components }}
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      - name: List nf-test files
-        id: list
-        uses: adamrtalbot/detect-nf-test-changes@v0.0.2
-        with:
-          head: ${{ github.sha }}
-          base: origin/${{ github.base_ref }}
-          include: .github/include.yaml
-
-      - name: print list of nf-test files
-        run: |
-          echo ${{ steps.list.outputs.components }}
-
   test:
-    name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})"
-    needs: [nf-test-changes]
-    if: needs.nf-test-changes.outputs.nf_test_files != '[]'
     runs-on: ubuntu-latest
+    name: "Test ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/5"
     strategy:
       fail-fast: false
       matrix:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
-        nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
-        profile:
-          - "conda"
-          - "docker"
-          - "singularity"
+        filter: ["process", "workflow", "function", "pipeline"]
+        profile: ["docker", "singularity"]
+        shard: [1, 2, 3, 4, 5]
         isMaster:
           - ${{ github.base_ref == 'master' }}
-        # Exclude conda and singularity on dev
         exclude:
-          - isMaster: false
-            profile: "conda"
           - isMaster: false
             profile: "singularity"
-          - profile: "conda"
-            nf_test_files: "tests/default.nf.test"
-          - profile: "conda"
-            nf_test_files: "tests/featurecounts_group_type.nf.test"
-          - profile: "conda"
-            nf_test_files: "tests/hisat2.nf.test"
-          - profile: "conda"
-            nf_test_files: "tests/kallisto.nf.test"
-          - profile: "conda"
-            nf_test_files: "tests/min_mapped_reads.nf.test"
-          - profile: "conda"
-            nf_test_files: "tests/remove_ribo_rna.nf.test"
-          - profile: "conda"
-            nf_test_files: "tests/salmon.nf.test"
-          - profile: "conda"
-            nf_test_files: "tests/skip_qc.nf.test"
-          - profile: "conda"
-            nf_test_files: "tests/skip_trimming.nf.test"
-          - profile: "conda"
-            nf_test_files: "tests/star_rsem.nf.test"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          architecture: "x64"
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -104,21 +62,6 @@ jobs:
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
-      - name: Set up Miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          conda-solver: libmamba
-          channels: conda-forge,bioconda
-
-      - name: Set up Conda
-        if: matrix.profile == 'conda'
-        run: |
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-
       - name: Install nf-test
         uses: nf-core/setup-nf-test@v1
         with:
@@ -137,14 +80,18 @@ jobs:
       - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run nf-test
+      - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5"
         run: |
-          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
-
-      - uses: pcolby/tap-summary@v1
-        with:
-          path: >-
-            test.tap
+          nf-test test \
+              --ci \
+              --debug \
+              --verbose \
+              --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
+              --shard ${{ matrix.shard }}/5 \
+              --changed-since HEAD^ \
+              --follow-dependencies \
+              --profile "+${{ matrix.profile }}" \
+              --filter ${{ matrix.filter }}
 
       - name: Output log on failure
         if: failure()

CHANGELOG.md

@@ -12,6 +12,7 @@ Special thanks to the following for their contributions to the release:
 - [Maxime Garcia](https://github.com/maxulysse)
 - [Jonathan Manning](https://github.com/pinin4fjords)
 - [Pablo Gonzalez de Aledo](https://github.com/pabloaledo)
+- [Edmund Miller](https://github.com/edmundmiller)
 
 ### Enhancements & fixes
 
@@ -22,6 +23,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1425](https://github.com/nf-core/rnaseq/pull/1425) - Add profile for ARM compatibility
 - [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release
 - [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers
+- [PR #1438](https://github.com/nf-core/rnaseq/pull/1438) - Implement @edmundmiller strategy for splitting up nf-test tests
 
 ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16