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

fix some small bugs that occur when running on some osx computers, an…

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

Workflow file for this run

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)