Candidate for 0.4.0 #33
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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 | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'Plant-Food-Research-Open/genepal') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| TEST_PARAMS: | |
| - minimal | |
| - short | |
| - nonmasked | |
| - stub | |
| OPTION_STUB: | |
| - "-stub" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run \ | |
| ${GITHUB_WORKSPACE} \ | |
| -profile docker \ | |
| -params-file \ | |
| ./tests/${{ matrix.TEST_PARAMS }}/params.json \ | |
| ${{ matrix.OPTION_STUB }} \ | |
| --outdir ./results \ | |
| --max_cpus 2 \ | |
| --max_memory '6.GB' \ | |
| --max_time '2.h' |