main_test.yaml

name: ashleys-qc-pipeline workflow checks

on:
  push:
    branches:
      - "**"

jobs:
Linting:
  runs-on: ubuntu-latest
  steps:
    - name: Checkout repository with 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 lfs pull'

    - name: Setup Python
      uses: actions/setup-python@v2

    - 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 snakemake-storage-plugin-http

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

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

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


  # Testing_ashleys_with_custom_python:
  #   # runs-on: self-hosted
  #   runs-on: ubuntu-latest
  #   steps:
  #     - name: Checkout repository with submodules and lfs
  #       uses: actions/checkout@v4
  #       with:
  #         submodules: recursive
  #         lfs: true
  #     - name: Setup Python
  #       uses: actions/setup-python@v2
  #     - 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 snakemake-storage-plugin-http
  #     - name: Run workflow
  #       run: |
  #         snakemake --cores 1 --software-deployment-method conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

  # Setting_slurm_cluster:
  #   runs-on: ubuntu-latest
  #   # For the action to work, you have to supply a mysql
  #   # service as defined below.
  #   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
  #       with:
  #         submodules: recursive
  #         lfs: true
  #     - name: Setup Python
  #       uses: actions/setup-python@v2
  #     - 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 snakemake-storage-plugin-http snakemake-executor-plugin-slurm
  #     - name: Run workflow
  #       run: |
  #         snakemake -j 1 -c 4 --executor slurm --workflow-profile .tests/config/slurm_config/ --software-deployment-method conda --conda-frontend mamba --configfile .tests/config/simple_config.yaml -p --snakefile workflow/Snakefile

  # WORK
  # Formatting:
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4

  #     - name: Formatting
  #       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:
  #     - uses: actions/checkout@v4
  #     - name: Linting
  #       uses: snakemake/snakemake-github-action@v1.24.0
  #       with:
  #         directory: .
  #         snakefile: ./workflow/Snakefile
  #         args: "--lint --config ashleys_pipeline=True"
  # Testing_ashleys:
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4
  #     - 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.yaml --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.yaml --conda-frontend mamba --report report.zip"

  # Testing_ashleys_fastqc_enabled:
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4
  #     - 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.yaml --config MultiQC=True --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.yaml --config MultiQC=True --conda-frontend mamba --report report.zip"

  # Testing_ashleys_ms_norm_enabled:
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4
  #     - 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.yaml --config multistep_normalisation=True --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.yaml --config multistep_normalisation=True --conda-frontend mamba --report report.zip"
  # Testing_ashleys_hg38:
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4
  #     - 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 --config reference=hg38 use_light_data=True chromosomes=[chr17] --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 --config reference=hg38 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
  # Testing_ashleys_hg19:
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4
  #     - 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 --config reference=hg19 use_light_data=True chromosomes=[chr17] --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 --config reference=hg19 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
  # Testing_ashleys_T2T:
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4
  #     - 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 --config reference=T2T use_light_data=True chromosomes=[chr17] --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 --config reference=T2T use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
  # Testing_ashleys_mm10:
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4
  #     - 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 --config reference=mm10 use_light_data=True chromosomes=[chr17] --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 --config reference=mm10 use_light_data=True chromosomes=[chr17] --conda-frontend mamba --report report.zip"
  # Testing_jub_nb:
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4
  #     - 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.yaml --config hand_selection=True --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.yaml --config hand_selection=True --conda-frontend mamba --report report.zip"
  # Testing_publishdir:
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4
  #     - 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.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.yaml --config publishdir=.tests/data_chr17_publishdir --conda-frontend mamba --report report.zip"
  # Testing_list_commands:
  #   runs-on: ubuntu-latest
  #   steps:
  #     - uses: actions/checkout@v4
  #     - name: Testing data
  #       uses: snakemake/snakemake-github-action@v1.24.0
  #       with:
  #         directory: .
  #         snakefile: ./workflow/Snakefile
  #         args: "--cores 1 --config list_commands=True --verbose --debug"