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| name: test | ||
| on: | ||
| push: | ||
| branches: | ||
| - before_read_from_file_commit | ||
| pull_request: | ||
| branches: | ||
| - before_read_from_file_commit | ||
| jobs: | ||
| test: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Install dependencies | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y samtools | ||
| sudo apt-get install -y nextflow | ||
| sudo apt-get install -y tr | ||
| sudo apt-get install -y gzip | ||
| - name: Setup miniconda | ||
| uses: conda-incubator/setup-miniconda@v3 | ||
| with: | ||
| auto-update-conda: true | ||
| # miniforge-variant: Mambaforge | ||
| channels: conda-forge, bioconda, defaults | ||
| auto-activate-base: true | ||
| use-mamba: true | ||
| - name: Checkout code | ||
| uses: actions/checkout@v4 | ||
| - name: Setup Nextflow | ||
| uses: nf-core/setup-nextflow@v2.0.0 | ||
| - name: Run test script | ||
| run: | | ||
| sudo apt-get install -y libxml2-utils samtools | ||
| bash run_test.sh | ||
