latest-dry-run #5
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| name: immediate_1 | |
| on: workflow_dispatch | |
| env: | |
| ASSCOM2_PROFILE: "profile/conda/local" | |
| 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: asscom2 | |
| environment-file: environment.yaml | |
| - name: check solution | |
| run: | | |
| mamba env export | |
| - name: test installation | |
| run: | | |
| python --version | |
| snakemake --version | |
| ./asscom2 --version | |
| ./asscom2 --help | |
| - name: dry run | |
| run: | | |
| ./asscom2 --config input_genomes="tests/E._faecium/*.fna" --dry-run | |
| - name: setup conda envs and copy | |
| run: | | |
| ./asscom2 --config input_genomes="tests/E._faecium/*.fna" --until copy && mamba clean --all -y | |
| - name: fast | |
| run: | | |
| ./asscom2 --config input_genomes="tests/E._faecium/*.fna" --until fast | |