feat: add gnomAD SV/CNV v4 support (#89) #217
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| Cancel-Previous: | |
| runs-on: ubuntu-latest | |
| if: github.ref != 'refs/heads/main' | |
| steps: | |
| - uses: khan/[email protected] | |
| with: | |
| workflows: "main.yml" | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| Formatting-Linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Setup formatting environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| init-shell: bash | |
| cache-environment: true | |
| post-cleanup: none # breaks otherwise | |
| - name: Check formating | |
| run: | | |
| make ci | |
| shell: bash -el {0} | |
| - name: Comment PR | |
| if: github.event_name == 'pull_request' && failure() | |
| uses: marocchino/[email protected] | |
| with: | |
| message: | | |
| Please check for formatting and linting issues. You can use `make lint` to: | |
| - Check your Bash style with `beautysh` and formatting with `shellcheck`. | |
| - Check your Python style with `black`, linting with `flake8`. | |
| - Check your Snakemake style with `snakefmt`. | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| Run-Test-Mode: | |
| needs: Formatting-Linting | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Setup formatting environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| init-shell: bash | |
| cache-environment: true | |
| post-cleanup: none # breaks otherwise | |
| - name: Install qsv (not in conda-forge yet) | |
| run: | | |
| cd /tmp | |
| wget https://github.com/jqnatividad/qsv/releases/download/0.112.0/qsv-0.112.0-x86_64-unknown-linux-musl.zip | |
| unzip qsv-0.112.0-x86_64-unknown-linux-musl.zip | |
| cp qsv_musl-1.2.3 /usr/local/bin/qsv | |
| - name: Install python package | |
| run: | | |
| pip install -e . | |
| shell: bash -el {0} | |
| - name: Run in test mode | |
| run: | | |
| CI=true snakemake --cores=1 -p all | |
| shell: bash -el {0} | |
| env: | |
| QSV_NO_UPDATE: "1" |