Add samplesheet to the gwas test-dataset #3
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| name: nf-test | |
| on: | |
| push: | |
| branches: | |
| - gwas | |
| pull_request: | |
| branches: | |
| - gwas | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "25.04.6" | |
| TEST_FILE: | |
| - tests/modules/generate_example_genotypes_vcfs.nf.test | |
| - tests/modules/concat_chunked_vcfs.nf.test | |
| - tests/modules/generate_pheno_cov.nf.test | |
| - tests/modules/extract_sample_ids.nf.test | |
| - tests/modules/chunk_vcfs.nf.test | |
| - tests/modules/index_chunked_vcfs.nf.test | |
| - tests/main.nf.test | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| - name: Run nf-test | |
| run: | | |
| mkdir -p reports | |
| nf-test test ${{ matrix.TEST_FILE }} --profile test --verbose --tap reports/test-results-${{ strategy.job-index }}.tap | |
| - name: List files for debugging | |
| run: ls -l . | |
| - name: Upload TAP reports | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: tap-reports-${{ matrix.NXF_VER }}-${{ strategy.job-index }} | |
| path: | | |
| reports/*.tap | |
| if-no-files-found: warn | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: nf-test-results-${{ matrix.NXF_VER }} | |
| path: | | |
| .nf-test.log |