testing.yml

name: Testing

on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]
  workflow_dispatch:

jobs:
    Testing:
      runs-on: ubuntu-latest
      steps:
      - uses: actions/checkout@v4
      - name: Set up Python 3.10
        uses: actions/setup-python@v5
        with:
          python-version: '3.10' 
      - name: Add conda to system path
        run: |
          # $CONDA is an environment variable pointing to the root of the miniconda directory
          echo $CONDA/bin >> $GITHUB_PATH
      - name: Install dependencies
        run: |
          conda install -c conda-forge mamba
      - name: Setup snakemake
        run: |
          mamba install -c conda-forge -c bioconda snakemake
      - run: echo "Finish installing snakemake"
      - name: unzip the files
        run: |
           gzip -d test_data/chr7.fa.gz
      - name: Run snakemake
        run: snakemake -s workflow/snakefile_final.smk --use-conda --rerun-incomplete --core 2 -k
      - name: Upload plot as artifact
        uses: actions/upload-artifact@v3
        with:
          name: plot
          path: /home/runner/work/isoworm/isoworm/R/ratio_BRAF.pdf