WIP: Add config customized for running CI on GH #2
Workflow file for this run
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| name: CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| - 260-improve-ci | |
| pull_request: | |
| release: | |
| types: [published] | |
| env: | |
| NXF_ANSI_LOG: false | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| # Only run on push if this is in the main repository | |
| if: "${{ github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/jasen' }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.10.1" | |
| parameters: | |
| - "-profile staphylococcus_aureus" | |
| - "-profile mycobacterium_tuberculosis" | |
| - "-profile klebsiella_pneumoniae" | |
| - "-profile escherichia_coli" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE}/main.nf ${{ matrix.parameters }} -config configs/nextflow.testrun.config --csv assets/test_data/samplelist.testrun.csv |