updated version of parsnp #137
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| name: ALPPACA CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| env: | |
| NXF_ANSI_LOG: false | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'NorwegianVeterinaryInstitute/ALPPACA') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # Nextflow versions | |
| include: | |
| # Test pipeline minimum Nextflow version | |
| - NXF_VER: "23.04.4" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Check out test data | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: NorwegianVeterinaryInstitute/ALPPACA | |
| ref: testdata | |
| path: testdata/ | |
| - name: where are we | |
| run: pwd | |
| - name: check schema content | |
| run: ls -R assets/ | |
| - name: Install Nextflow | |
| env: | |
| NXF_VER: ${{ matrix.NXF_VER }} | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run ani track test | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_ani,docker --out_dir ./results | |
| - name: Run cgmlst track test | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_cgmlst,docker --schema ${{ github.workspace }}/assets/data/test_schema/ --out_dir ./results | |
| - name: Run core genome track test | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_core_genome,docker --out_dir ./results | |
| - name: Run core gene track test | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_core_gene,docker --out_dir ./results | |
| - name: Run mapping track test | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_mapping,docker --out_dir ./results |