fix some small bugs that occur when running on some osx computers, an… #3
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| 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) |