Release 3.0.2 #1242
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 | |
| 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 the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnafusion') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| trim_parameters: | |
| - "--fastp_trim false" | |
| - "--fastp_trim true" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Dry test build | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub --build_references \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --all \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ | |
| --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} | |
| - name: Dry test run | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --all ${{ matrix.trim_parameters }} \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references |