Integrated nf-test into pipeline CI #49
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: | |
| env: | |
| NXF_ANSI_LOG: false | |
| 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: | |
| nf-test-changes: | |
| name: Check for changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| nf_test_files: ${{ steps.list.outputs.components }} | |
| steps: | |
| - uses: actions/[email protected] | |
| with: | |
| fetch-depth: 0 | |
| - name: List nf-test files | |
| id: list | |
| uses: adamrtalbot/[email protected] | |
| 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: ${{ 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 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] | |
| profile: | |
| - "docker" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/[email protected] | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - uses: actions/[email protected] | |
| 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/[email protected] | |
| with: | |
| version: 0.9.0 | |
| - name: Disk space cleanup | |
| if: matrix.nf_test_files == 'tests/stub/main.nf.test' | |
| uses: jlumbroso/[email protected] | |
| - name: Run nf-test | |
| run: | | |
| nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: [test] | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: ${{ !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |