latest-dry-run #7
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: latest-dry-run | |
| on: workflow_dispatch | |
| env: | |
| COMPAREM2_PROFILE: "profile/conda/default" | |
| jobs: | |
| create-env: | |
| name: ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v2 | |
| - name: create environment with mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda,defaults | |
| auto-activate-base: false | |
| activate-environment: comparem2_launcher | |
| environment-file: environment.yaml | |
| - name: check solution | |
| run: | | |
| mamba env export | |
| - name: test installation | |
| run: | | |
| python --version | |
| snakemake --version | |
| ./comparem2 --version | |
| ./comparem2 --help | |
| - name: dry run | |
| run: | | |
| unzip tests/E._faecium/fna.zip | |
| ./comparem2 --config input_genomes="*.fna" --dry-run |