Update all nf-core modules and subworkflows #787
Workflow file for this run
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| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| name: nf-core CI | |
| on: | |
| pull_request: | |
| release: | |
| types: [published] | |
| merge_group: | |
| types: | |
| - checks_requested | |
| branches: | |
| - master | |
| - dev | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFT_VER: "0.8.3" | |
| 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: | |
| changes: | |
| name: Check for changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'tags' output variable | |
| tags: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Combine all tags.yml files | |
| id: get_username | |
| run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | |
| - name: debug | |
| run: cat .github/tags.yml | |
| - uses: dorny/paths-filter@v2 | |
| id: filter | |
| with: | |
| filters: ".github/tags.yml" | |
| 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-everything"]' | tee -a $GITHUB_OUTPUT | |
| else | |
| echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT | |
| fi | |
| test: | |
| name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} | |
| needs: [changes, define_nxf_versions] | |
| if: needs.changes.outputs.tags != '[]' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} | |
| tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] | |
| profile: | |
| - "docker" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - 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 | |
| - name: Cache nf-test installation | |
| id: cache-software | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/local/bin/nf-test | |
| /home/runner/.nf-test/nf-test.jar | |
| key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest | |
| - name: Install nf-test | |
| if: steps.cache-software.outputs.cache-hit != 'true' | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: Run nf-test | |
| run: | | |
| nf-test test --verbose --tag ${{ matrix.tags }} --profile "${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap | |
| - uses: pcolby/tap-summary@v1 | |
| with: | |
| path: >- | |
| test.tap | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log | |
| - 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 |