v2.0.0-beta.3 #24
Workflow file for this run
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: 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 }} |