v2.0.0-beta.1 #22
Workflow file for this run
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| name: test conda profiles on demand and on publish | |
| on: | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| jobs: | |
| preload_ancestry: | |
| uses: ./.github/workflows/preload-reference.yml | |
| test_mamba_ancestry: | |
| uses: ./.github/workflows/ancestry-conda.yml | |
| needs: [preload_ancestry] | |
| with: | |
| ancestry-cache-key: ${{ needs.preload_ancestry.outputs.cache-key }} | |
| test_mamba_standard: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| test_profile: ["test"] | |
| profile: ["mamba"] | |
| nxf_ver: ["23.10.0", ""] | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| channels: conda-forge,bioconda,defaults | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| python-version: "3.10" | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'corretto' | |
| java-version: '17' | |
| - name: install nxf | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_profile}},${{ matrix.profile }} |