test_action.yml

name: hadge test workflow
on:
  push:
  pull_request:
jobs:
  test_genetic:
    name: Run pipeline in genetic mode with test data
    runs-on: ubuntu-latest
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v4
      - 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: "3.11"
          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 --mode genetic --souporcell False --generate_anndata False
  test_hashing:
    name: Run pipeline in hashing mode 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: "3.11"
          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 --mode hashing --generate_anndata False