donot match #43
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |