Update samshee #734
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| name: nf-core CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| pull_request: | |
| branches: | |
| - dev | |
| - master | |
| release: | |
| types: [published] | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFT_VER: "0.9.0" | |
| NFT_WORKDIR: "~" | |
| NFT_DIFF: "pdiff" | |
| NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| define_nxf_versions: | |
| name: Choose nextflow versions to test against depending on target branch | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.nxf_versions.outputs.matrix }} | |
| steps: | |
| - id: nxf_versions | |
| run: | | |
| if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then | |
| echo matrix='["latest-stable"]' | tee -a $GITHUB_OUTPUT | |
| else | |
| echo matrix='["latest-stable", "23.04.0"]' | tee -a $GITHUB_OUTPUT | |
| fi | |
| test: | |
| name: Run pipeline with test data | |
| needs: define_nxf_versions | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| shard: [1, 2, 3, 4, 5, 6] | |
| NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} | |
| profile: ["docker"] | |
| env: | |
| SHARDS: "6" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| architecture: "x64" | |
| - name: Install pdiff to see diff between nf-test snapshots | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pdiff | |
| - uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: ${{ env.NFT_VER }} | |
| - name: Run Tests (Shard ${{ matrix.shard }}/${{ env.SHARDS }}) | |
| run: | | |
| nf-test test \ | |
| --ci \ | |
| --shard ${{ matrix.shard }}/${{ env.SHARDS }} \ | |
| --changed-since HEAD^ \ | |
| --profile "+${{ matrix.profile }}" \ | |
| --filter pipeline \ | |
| --junitxml=test.xml | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v3 | |
| if: always() # always run even if the previous step fails | |
| with: | |
| report_paths: test.xml | |
| annotate_only: true |