run_quick_tests.yaml

name: Run quick tests of pipeline

on:
  pull_request:
    branches:
      - master
  workflow_dispatch:

jobs:
  run-tests:
    runs-on: ubuntu-latest
    container:
      image: rocker/r-ver:4.1.0
      options: --privileged

    steps:
      - name: Checkout repository
        uses: actions/checkout@v3

      - name: Setup Singularity
        uses: eWaterCycle/setup-singularity@v7
        with:
          singularity-version: 3.8.3

      - name: Download Singularity container
        run: |
          singularity pull library://opain/genopred/genopred_pipeline:latest

      - name: Set environment variables
        run: |
          echo "SIF_FILE=$GITHUB_WORKSPACE/genopred_pipeline_latest.sif" >> $GITHUB_ENV
          if [ "${{ github.event_name }}" = "pull_request" ]; then
            echo "BRANCH_NAME=${{ github.head_ref }}" >> $GITHUB_ENV
          else
            echo "BRANCH_NAME=${{ github.ref_name }}" >> $GITHUB_ENV
          fi
          
      - name: Install R dependencies
        run: |
          Rscript -e 'install.packages("testthat", repos="https://cran.rstudio.com/")'
          Rscript -e 'install.packages("data.table", repos="https://cran.rstudio.com/")'
          Rscript -e 'install.packages("R.utils", repos="https://cran.rstudio.com/")'

      - name: Run tests
        run: |
          Rscript -e "testthat::test_dir('pipeline/tests/testthat')"
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
          SIF_FILE: ${{ env.SIF_FILE }}
          BRANCH_NAME: ${{ env.BRANCH_NAME }}

      - name: Setup tmate session
        if: ${{ failure() }}
        uses: mxschmitt/action-tmate@v3
        timeout-minutes: 60