wdl_checker.yml

name: MiniWDL linter CI

on:
  push:
  workflow_dispatch:

jobs:
  run-miniwdl:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout repository
      uses: actions/checkout@v2

    - name: Set up Python
      uses: actions/setup-python@v2
      with:
        python-version: '3.8' # specify the Python version you need

    - name: Install Docker
      run: |
        curl -fsSL https://get.docker.com -o get-docker.sh
        sh get-docker.sh
        sudo usermod -aG docker $USER

    - name: Build Docker Image
      run: |
        docker build -t local-metams:latest .

    - name: Install MiniWDL
      run: |
        python -m pip install --upgrade pip
        pip install miniwdl

    - name: Test Lipid MiniWDL
      run: |
        miniwdl run wdl/metaMS_lipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files

    - name: Test GCMS MiniWDL
      run: |
        # Add the commands to run your MiniWDL workflow
        miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms.json --verbose --no-cache --copy-input-files