New module: Kraken2/Bracken on Unaligned Sequences for Contamination Detection #2973
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_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: | |
| 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/[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: | |
| - "latest-everything" | |
| - "23.04" | |
| nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] | |
| profile: | |
| - "docker" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ 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 | |
| - uses: nf-core/setup-nf-test@v1 | |
| - name: Run nf-test | |
| 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 | |
| - 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 | |
| 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) }}" |