contig: Add strobealign-aemb method. #118
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| name: Test CoverM with Setup-Miniconda From Marketplace | |
| on: [push, pull_request] | |
| jobs: | |
| miniconda_linux: | |
| name: Miniconda (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: coverm.yml | |
| channels: conda-forge,defaults,bioconda | |
| mamba-version: "*" | |
| - name: Conda info | |
| shell: bash -el {0} | |
| run: conda info | |
| - name: Conda list | |
| shell: pwsh | |
| run: conda list | |
| - name: Run test | |
| shell: bash -el {0} | |
| run: | | |
| cargo test | |
| miniconda_osx: | |
| name: miniconda_osx (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["macos-latest"] | |
| python-version: ["3.8"] # Must use 3.8 so that minimap2 installs | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: coverm-osx.yml | |
| channels: conda-forge,defaults,bioconda | |
| mamba-version: "*" | |
| - name: Conda info | |
| shell: bash -el {0} | |
| run: conda info | |
| - name: Conda list | |
| shell: pwsh | |
| run: conda list | |
| - name: Run test | |
| shell: bash -el {0} | |
| run: | | |
| cargo test -- --skip bwa_mem2 --skip strobealign |