add singularity #621
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| - main | |
| - ci | |
| pull_request: | |
| branches: | |
| - dev | |
| - main | |
| release: | |
| types: [published] | |
| jobs: | |
| preload_containers: | |
| uses: ./.github/workflows/preload-containers.yml | |
| test: | |
| needs: preload_containers | |
| name: Run standard workflow test | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| test_profile: ["test"] | |
| profile: ["docker"] | |
| nxf_ver: ['22.10.0', ''] # minimum supported version, latest version | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: ${{ matrix.nxf_ver }} | |
| - name: Restore docker cache | |
| id: restore-docker | |
| uses: actions/cache@v3 | |
| if: matrix.profile == 'docker' | |
| with: | |
| path: ${{ runner.temp }}/docker | |
| key: ${{ needs.preload_docker.outputs.docker-cache-key }} | |
| - name: Load docker images from cache | |
| if: steps.restore-docker.outputs.cache-hit == 'true' | |
| run: | | |
| find $HOME -name '*.tar' | |
| find ${{ runner.temp }}/docker/ -name '*.tar' -exec sh -c 'docker load < {}' \; | |
| - name: Run pipeline with test data | |
| continue-on-error: false | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_profile}},${{ matrix.profile }} | |