latest-dry-run #19
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| 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: "<2" | |
| 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 --help | |
| ./comparem2 --version | |
| ./comparem2 --cite | |
| ./comparem2 --status | |
| - name: dry run | |
| run: | | |
| ./comparem2 --dry-run | |
| touch dummy_1.fa; ./comparem2 --dry-run | |
| touch dummy_2.fa; ./comparem2 --dry-run | |
| touch dummy_3.fa; ./comparem2 --dry-run | |
| unzip tests/E._faecium/fna.zip | |
| ./comparem2 --config input_genomes="*.fna" --dry-run | |
| ./comparem2 --config input_genomes="*.fna" --until fast --dry-run | |
| ./comparem2 --config input_genomes="*.fna" --until isolate --dry-run | |
| ./comparem2 --config input_genomes="*.fna" --until meta --dry-run | |
| ./comparem2 --config input_genomes="*.fna" --until downloads --dry-run | |
| ls dummy_{2,3}.fa > fofn.txt; ./comparem2 --config fofn="fofn.txt" --dry-run | |