run_snakemake.yaml

name: Build
run-name: ${{ github.actor }} testing Snakemake workflow 🚀
on:
  pull_request:
    types: [opened, reopened]
defaults:
  run:
    shell: bash -l {0}
jobs:
  Run-Snakemake-workflow:
    runs-on: ubuntu-latest
    steps:
      - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event. "
      - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!"
      - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
      - name: Check out repository code
        uses: actions/checkout@v3
      - run: echo "💡 The ${{ github.repository }} repository has been cloned to the runner."
      - run: echo "🖥️ The workflow is now ready to test your code on the runner."
      - name: Install Conda environment from environment.yml
        uses: mamba-org/provision-with-micromamba@main 
        with:
          environment-file: .github/environment.yml
      - name: Downlaod hg38 ref file
        run: |
          wget --directory-prefix=test/ref/ https://www.bcgsc.ca/downloads/genomes/9606/hg38_no_alt/bwa_0.7.6a_ind/genome/hg38_no_alt.fa 
      - name: Download snpEff
        run: |
          wget --directory-prefix=test/ref https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.99.zip
          unzip test/ref/snpEff_v5_0_GRCh38.99.zip -d test/ref/
          mv test/ref/data test/ref/snpeff
      - name: Run workflow
        run: | 
          snakemake -c 1 --use-singularity --configfiles test/config/defaults.yaml test/config/parameters.yaml test/config/samples.yaml 
      - name: Check output
        run: |
          ls -lt output/exampleSample/
      - run: echo "🍏 This job's status is ${{ job.status }}."