28 change hdr to hrd #15
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: Main | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| - 15-cicd-tests | |
| pull_request: | |
| release: | |
| types: [published] | |
| # Uncomment if we need an edge release of Nextflow again | |
| # env: NXF_EDGE: 1 | |
| jobs: | |
| test: | |
| name: Run workflow tests | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| # Nextflow versions: check pipeline minimum and current latest | |
| nxf_ver: ["22.10.6"] | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| env: | |
| CAPSULE_LOG: none | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: HELPTEXT Run with the help flag | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} --help | |
| - name: DELAY to try address some odd behaviour with what appears to be a conflict between parallel htslib jobs leading to CI hangs | |
| run: | | |
| if [[ $NXF_VER = '' ]]; then sleep 1200; fi | |
| - name: BASIC Run the basic pipeline only for ACE calling with docker | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker |