Some modifications made to Hadge that were esential for running large scale processing of Onek1k data #49
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| name: hadge test workflow | |
| on: push | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| miniconda-version: "latest" | |
| channels: conda-forge, bioconda | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Set up Python to install gdown | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.9" | |
| cache: "pip" | |
| - name: Download test dataset | |
| run: bash ${GITHUB_WORKSPACE}/test_data/download_data.sh | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,conda --souporcell False --generate_anndata False |