main_test.yaml

name: ashleys-qc-pipeline workflow 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 without submodules
        uses: actions/checkout@v4.1.7

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

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

      - 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

  # Testing-basic-with-slurm:
  #   runs-on: ubuntu-latest
  #   needs:
  #     - Formatting
  #     - Linting
  #     - Testing-basic
  #   services:
  #     mysql:
  #       image: mysql:8.0
  #       env:
  #         MYSQL_ROOT_PASSWORD: root
  #       ports:
  #         - "8888:3306"
  #       options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3

  #   steps:
  #     - uses: actions/checkout@v3

  #     - uses: koesterlab/setup-slurm-action@v1

  #     - 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: 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 with SLURM support
  #       run: mamba install -c conda-forge -c bioconda snakemake==7.32.4

  #     - name: Run workflow on SLURM
  #       run: |
  #         snakemake -j 1 -c 1 --executor slurm --workflow-profile .tests/config/slurm_config/ \
  #         --use-conda --conda-frontend mamba --configfile .tests/config/simple_config_ashleys.yaml -p --snakefile workflow/Snakefile

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

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

      - 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: 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 --config MultiQC=True \
          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

  Testing-with-ms-norm:
    runs-on: ubuntu-latest
    needs:
      - Formatting
      - Linting
      - Testing-basic
    steps:
      - name: Checkout repository with submodules
        uses: actions/checkout@v4.1.7
        with:
          submodules: recursive

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

      - 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: 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 --config multistep_normalisation=True \
          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

  Testing-with-hg38:
    runs-on: ubuntu-latest
    needs:
      - Formatting
      - Linting
      - Testing-basic
    # - Testing-basic-with-slurm
    steps:
      - name: Checkout repository with submodules
        uses: actions/checkout@v4.1.7
        with:
          submodules: recursive

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

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

      - name: Run workflow
        run: |
          snakemake --cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] \
          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

  Testing-with-hg19:
    runs-on: ubuntu-latest
    needs:
      - Formatting
      - Linting
      - Testing-basic
    # - Testing-basic-with-slurm
    steps:
      - name: Checkout repository with submodules
        uses: actions/checkout@v4.1.7
        with:
          submodules: recursive

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

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

      - name: Run workflow
        run: |
          snakemake --cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] \
          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

  Testing-with-T2T:
    runs-on: ubuntu-latest
    needs:
      - Formatting
      - Linting
      - Testing-basic
    # - Testing-basic-with-slurm
    steps:
      - name: Checkout repository with submodules
        uses: actions/checkout@v4.1.7
        with:
          submodules: recursive

      - 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: 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 --config reference=T2T use_light_data=True chromosomes=[chr17] \
          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

  Testing-with-mm10:
    runs-on: ubuntu-latest
    needs:
      - Formatting
      - Linting
      - Testing-basic
    # - Testing-basic-with-slurm
    steps:
      - name: Checkout repository with submodules
        uses: actions/checkout@v4.1.7
        with:
          submodules: recursive

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

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

      - name: Run workflow
        run: |
          snakemake --cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] \
          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

  # Testing_publishdir:
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4.1.7
  #     - name: Testing data
  #       uses: snakemake/snakemake-github-action@v1.24.0
  #       with:
  #         directory: .
  #         snakefile: ./workflow/Snakefile
  #         stagein: "conda config --set channel_priority flexible"
  #         args: "--cores 1 --use-conda --configfile .tests/config/simple_config_ashleys.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba -p --verbose --debug"
  #     - name: Testing report
  #       uses: snakemake/snakemake-github-action@v1.24.0
  #       with:
  #         directory: .
  #         snakefile: ./workflow/Snakefile
  #         args: "--cores 1 --use-conda --configfile .tests/config/simple_config_ashleys.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba --report report.zip"