Last fixes before v0.1.0 release #285
Workflow file for this run
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: | |
| 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/ |