Fix vep container issue #174
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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'CenterForMedicalGeneticsGhent/nf-cmgg-structural') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "22.10.5" | |
| - "latest-everything" | |
| test: | |
| - "all_annotate" | |
| - "sv_no_annotate" | |
| - "smoove" | |
| - "delly" | |
| - "manta" | |
| - "expansionhunter" | |
| - "qdnaseq" | |
| - "wisecondorx" | |
| steps: | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| # TODO remove the version pinning once nf-test outputDir bug is fixed | |
| - name: Install nf-test | |
| run: | | |
| conda install -c bioconda nf-test==0.7.3 | |
| - 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" |