testing.yml

name: Tests

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

jobs:
  test_preprocessr:
    runs-on: ubuntu-latest
    
    steps:
      - uses: actions/checkout@v4
      - name: make test
        run: make -C src test

  test_strainr:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - uses: r-lib/actions/setup-r@v2
    - uses: r-lib/actions/setup-r-dependencies@v2
      with:
        cache-version: 1
        r-version: 'release'
        packages: |
          any::tidyverse
          any::optparse

    - name: Plot.R test
      run: |
        ./src/Plot.R -a tests/inputs/ -i tests/inputs/ -p testing
        diff tests/inputs/testing_abundance_summary.tsv \
          tests/expected_output/expected_abundance_summary.tsv
        rm tests/inputs/testing_abundance_summary.tsv
      shell: bash

  test_comprehensive:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: conda-incubator/setup-miniconda@v3
      - name: test run comp
        shell: bash -el {0}
        run: |
          conda install -c bioconda -c conda-forge -y strainr2
          conda remove --force -y strainr2
          make -C src release
          export PATH="$(pwd)/src/:$PATH"
          PreProcessR -i tests/genomes/mixture -o tests/StrainR2DB_testing
          diff <(sort tests/StrainR2DB_testing/KmerContent.report) <(sort tests/expected_output/KmerContent_comprehensive.report)
          StrainR -1 tests/inputs/mock_reads_testing_R1.fastq.gz \
            -2 tests/inputs/mock_reads_testing_R2.fastq.gz \
            -r tests/StrainR2DB_testing -o tests/StrainR2_out_testing -p testing -t 1
          diff <(sort tests/StrainR2_out_testing/testing.abundances) <(sort tests/expected_output/testing_comprehensive.abundances)
          diff <(sort tests/StrainR2_out_testing/testing_abundance_summary.tsv) <(sort tests/expected_output/abundance_summary_comprehensive.tsv)