Add option to name cached BAM outputs #217
Workflow file for this run
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| name: Test CoverM with Pixi | |
| on: [push, pull_request] | |
| jobs: | |
| pixi_test_dependencies_locked: | |
| name: Pixi test_dependencies_locked (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Pixi | |
| run: | | |
| curl -fsSL https://pixi.sh/install.sh | bash | |
| echo "$HOME/.pixi/bin" >> $GITHUB_PATH | |
| - name: Show environment info | |
| run: | | |
| pixi run --frozen pixi info | |
| pixi run --frozen pixi list | |
| - name: Run tests with Pixi | |
| run: | | |
| pixi run --frozen cargo test | |
| # Run after removing lock file so dependences are unlocked | |
| pixi_test_dependencies_optimistic: | |
| name: Pixi test_dependencies_optimistic (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Pixi | |
| run: | | |
| curl -fsSL https://pixi.sh/install.sh | bash | |
| echo "$HOME/.pixi/bin" >> $GITHUB_PATH | |
| - name: Remove lock file | |
| run: | | |
| rm -fv pixi.lock | |
| - name: Create environment | |
| run: | | |
| pixi run pixi info | |
| - name: Show environment info | |
| run: | | |
| pixi run pixi list | |
| - name: Run tests with Pixi | |
| run: | | |
| pixi run cargo test | |
| # OSX tests | |
| pixi_test_dependencies_locked_osx: | |
| name: Pixi test_dependencies_locked (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["macos-latest"] | |
| python-version: ["3.8"] # Must use 3.8 so that minimap2 installs | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Pixi | |
| run: | | |
| curl -fsSL https://pixi.sh/install.sh | bash | |
| echo "$HOME/.pixi/bin" >> $GITHUB_PATH | |
| - name: Show environment info | |
| run: | | |
| pixi run --frozen pixi info | |
| pixi run --frozen pixi list | |
| - name: Run tests with Pixi | |
| run: | | |
| pixi run --frozen cargo test -- --skip bwa_mem2 --skip strobealign | |
| # Run after removing lock file so dependences are unlocked | |
| pixi_test_dependencies_optimistic_osx: | |
| name: Pixi test_dependencies_optimistic (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["macos-latest"] | |
| python-version: ["3.8"] # Must use 3.8 so that minimap2 installs | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Pixi | |
| run: | | |
| curl -fsSL https://pixi.sh/install.sh | bash | |
| echo "$HOME/.pixi/bin" >> $GITHUB_PATH | |
| - name: Remove lock file | |
| run: | | |
| rm -fv pixi.lock | |
| - name: Create environment | |
| run: | | |
| pixi run pixi info | |
| - name: Show environment info | |
| run: | | |
| pixi run pixi list | |
| - name: Run tests with Pixi | |
| run: | | |
| pixi run cargo test -- --skip bwa_mem2 --skip strobealign |