main.yml

# This is a basic workflow to help you get started with Actions

name: CI

# Controls when the workflow will run
on:
  # Triggers the workflow on push or pull request events but only for the master branch
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:

  build_and_test:
    runs-on: ubuntu-latest
    steps:
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - uses: actions/checkout@v2
      - uses: actions/setup-python@v2
    
      - name: Install STRetch 
        run: |
          ./.testing/install-ci.sh
          mkdir test
          cp reference-data/SCA8_region.bed test/
          pwd
          ls

    
      - name: "Set environmental variables"
        run: |
          echo "STRetch=$GITHUB_WORKSPACE" >> $GITHUB_ENV
          
      - name: End to end test
        run: |
          echo $STRetch
          pwd
          ls
          cd $STRetch/test/
          ../tools/bin/bpipe run ../pipelines/STRetch_exome_pipeline.groovy ../test-data/*.fastq.gz
      
      
      - name: Unit tests
        run: |
          cd $STRetch/scripts/tests/
          source $STRetch/tools/miniconda/bin/activate $STRetch/tools/miniconda/envs/STR
          python -m pytest test_*.py

      - name: View output files
        run: |
          cd $STRetch/test/
          diff STRs.tsv ../.testing/STRs.benchmark.tsv
          head *.locus_counts *.STR_counts *.median_cov
          head *.tsv
          
          
      - name: Calculate and display code coverage
        run: |
          source $STRetch/tools/miniconda/bin/activate $STRetch/tools/miniconda/envs/STR
          cd $STRetch/scripts/tests/
          coverage run -m pytest test_*.py
          bash <(curl -s https://codecov.io/bash) -s .