github-actions.yml

name: DeepRVAT
run-name: DeepRVAT 🧬🧪💻🧑‍🔬
on: [ push ]
jobs:
  DeepRVAT-Pipeline-Smoke-Tests:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository code
        uses: actions/checkout@v3
      - name: Training Association Testing smoke test
        uses: snakemake/snakemake-github-action@v1.24.0
        with:
          directory: 'example'
          snakefile: 'pipelines/training_association_testing.snakefile'
          args: '-j 1 -n'
          stagein: 'pip install -e ${{ github.workspace }}'
      - name: Seed Gene Discovery Smoke Test
        uses: snakemake/snakemake-github-action@v1.24.0
        with:
          directory: 'example'
          snakefile: 'pipelines/seed_gene_discovery.snakefile'
          args: '-j 1 -n'
      - name: Link pretrained models
        run: cd ${{ github.workspace }}/example && ln -s ../pretrained_models
      - name: Association Testing Pretrained Smoke Test
        uses: snakemake/snakemake-github-action@v1.24.0
        with:
          directory: 'example'
          snakefile: 'pipelines/association_testing_pretrained.snakefile'
          args: '-j 1 -n'