main_test.yaml

name: MosaiCatcher basic checks

on:
  push:
    branches:
      - "**"
      
jobs:

  Formatting:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4.1.7

      - name: Formatting using Super-Linter
        uses: github/super-linter@v4
        env:
          VALIDATE_ALL_CODEBASE: false
          DEFAULT_BRANCH: master
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          VALIDATE_SNAKEMAKE_SNAKEFMT: true


  Linting:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository with submodules
        uses: actions/checkout@v4.1.7
        with:
          submodules: 'recursive'  # Ensures all submodules are checked out
          lfs: true                # Ensures LFS objects for the main repo are pulled

      - name: Pull LFS objects in submodules
        run: |
          git submodule foreach --recursive 'git lfs pull'

      - name: List contents of .tests
        run: |
          tree -h .tests

      - name: List contents of workflow/data
        run: |
          tree -h workflow/data

      - name: Setup Python
        uses: actions/setup-python@v5 
        with:
          python-version: '3.12' 

      - name: Add Conda to system path
        run: |
          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==7.32.4

      - name: Run Snakemake Lint
        run: |
          snakemake --lint

  Testing-basic:
    runs-on: ubuntu-latest
    # needs: 
    #   - Formatting
    #   - Linting
    steps:
      - name: Checkout repository with submodules and LFS
        uses: actions/checkout@v4.1.7
        with:
          submodules: recursive
          lfs: true

      - name: Pull LFS objects in submodules
        run: git submodule foreach --recursive 'git lfs pull'

      - name: Setup Python
        uses: actions/setup-python@v5 
        with:
          python-version: '3.12' 

      - name: List contents of .tests
        run: |
          tree -h .tests

      - name: Show config file
        run: |
          cat .tests/config/simple_config_ashleys.yaml

      - name: List contents of workflow/data
        run: |
          tree -h workflow/data

      - name: Add Conda to system path
        run: 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==7.32.4

      - name: List options of workflow
        run: |
          snakemake --cores 1 --config list_commands=True --verbose --debug

      - name: Run workflow
        run: |
          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_ashleys.yaml \
          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile