test.yml

name: Test Pipeline Components

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]

jobs:
  test:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:
    - uses: actions/checkout@v3

    - name: Set up Conda
      uses: conda-actions/setup-conda@v2
      with:
        python-version: '3.10'

    - name: Cache Conda env
      uses: actions/cache@v3
      with:
        path: |
          /usr/share/miniconda/envs/
        key: conda-${{ hashFiles('environment.yml') }}
        restore-keys: |
          conda-

    - name: Create Conda environment
      run: conda env create -f environment.yml

    - name: Run syntax checks
      run: |
        conda activate taxonomy-pipeline
        
        # Check Perl scripts syntax
        echo "Checking Perl scripts syntax..."
        for script in workflow/scripts/*.pl; do
          echo "Checking $script"
          perl -cw $script
        done
        
        # Run Perl::Critic on scripts
        echo "Running Perl::Critic..."
        for script in workflow/scripts/*.pl; do
          echo "Analyzing $script"
          perlcritic --gentle $script
        done
        
        # Validate Snakefile syntax
        echo "Checking Snakefile syntax..."
        snakemake --lint
        
        # Test Snakemake dry run with minimal test data
        echo "Testing Snakefile dry run..."
        snakemake -n

    - name: Run unit tests
      run: |
        conda activate taxonomy-pipeline
        cd tests
        prove -v *.t