files added #2
Workflow file for this run
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| 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 | |
| - name: BASIC Run the basic pipeline only for ACE calling with singularity | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,singularity |