main.yaml

name: MosaiCatcher basic checks

on:
  push:
    branches:
      - "**"
  schedule:
    - cron: "0 0 * * 0"
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 without submodules
        uses: actions/checkout@v4
        # 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 pull origin main'

      - name: List contents of .tests-mock
        run: |
          tree -h github-actions-runner/.tests-mock

      - 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 --config data_location=github-actions-runner/.tests-mock/data_CHR17 --lint

  Testing-basic-v7:
    runs-on: ubuntu-latest
    # needs:
    #   - Formatting
    #   - Linting
    steps:
      - name: Checkout repository with submodules
        uses: actions/checkout@v4
        with:
          submodules: recursive

      # Update references
      - name: Git Submodule Update
        run: |
          # git pull --recurse-submodules
          git submodule update --remote --recursive --force --init

      - 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_mosaicatcher.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_mosaicatcher.yaml \
          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

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

      - name: Git Submodule Update
        run: |
          # git pull --recurse-submodules
          git submodule update --remote --recursive --force --init

      - 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_mosaicatcher.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_mosaicatcher.yaml --config ashleys_pipeline=True \
          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile