Bug/sex determination #326
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: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| env: | |
| NXF_ANSI_LOG: false | |
| AWS_ACCESS_KEY_ID: ${{ secrets.UGENT_S3_ACCESS_KEY }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.UGENT_S3_SECRET_KEY }} | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test_all: | |
| name: Run nf-test with ${{ matrix.test }}-${{ matrix.NXF_VER }} | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-cmgg/structural') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.10.0" | |
| - "latest-everything" | |
| test: | |
| - "pipeline_sv" | |
| - "pipeline_cnv" | |
| - "pipeline_repeats" | |
| - "pipeline_duplicates" | |
| - "pipeline_families" | |
| - "bam_cnv_calling" | |
| - "bam_prepare_samtools" | |
| - "bam_repeat_estimation_expansionhunter" | |
| - "bam_sv_calling" | |
| - "bam_variant_calling_delly" | |
| # - "bam_variant_calling_gridss" | |
| - "bam_variant_calling_manta" | |
| - "bam_variant_calling_qdnaseq" | |
| - "bam_variant_calling_smoove" | |
| - "bam_variant_calling_wisecondorx" | |
| - "vcf_annotate_vep_annotsv_vcfanno" | |
| - "vcf_concat_bcftools" | |
| - "vcf_merge_callers_jasmine" | |
| - "vcf_merge_family_jasmine" | |
| steps: | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| - name: Check out pipeline code | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Install nf-test | |
| run: | | |
| conda install -c bioconda nf-test | |
| - name: Run pipeline with test data | |
| run: | | |
| $CONDA/bin/nf-test test --tag ${{ matrix.test }} --junitxml=default.xml | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v3 | |
| if: always() # always run even if the previous step fails | |
| with: | |
| report_paths: "default.xml" | |
| - name: Upload log file artifact | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: nf-test-workdir | |
| path: .nf-test/ |