Updated PFR's Kraken 2 and started using _JAVA_OPTIONS in RUNASSEMBLYVISUALIZER #200
Workflow file for this run
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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: | |
| 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) }}" |