Real-data pytests #16
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| name: pytest | |
| on: [pull_request, push] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| test_mRNA: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-file: snakePipes/shared/rules/envs/rna_seq.yaml | |
| environment-name: rnaseqenv | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| channel_priority: 'strict' | |
| cache-downloads: true | |
| post-cleanup: 'none' | |
| - name: create_starix | |
| run: | | |
| micromamba activate rnaseqenv | |
| gunzip -c tests/data/genomes/genome_chr17.fa.gz > genome_chr17.fa | |
| gunzip -c tests/data/genomes/genes_chr17.gtf.gz > genes_chr17.gtf | |
| STAR --runThreadN 4 --runMode genomeGenerate --genomeDir tests/data/mRNA_STAR --genomeFastaFiles genome_chr17.fa --sjdbGTFfile genes_chr17.gtf --sjdbOverhang 100 --genomeSAindexNbases 12 | |
| - uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-file: .github/snakePipesEnvCI.yml | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| channel_priority: 'strict' | |
| cache-downloads: true | |
| - name: Install snakePipes | |
| run: | | |
| micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv | |
| - name: pytest | |
| run: | | |
| micromamba activate snakePipes_CI | |
| snakePipes config --tempDir /tmp --condaEnvDir ./ | |
| snakePipes createEnvs --only CONDA_SHARED_ENV CONDA_RNASEQ_ENV | |
| pytest --verbosity=2 -rP tests/test_mRNA.py | |
| CI_jobcounts: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-file: .github/snakePipesEnvCI.yml | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| channel_priority: 'strict' | |
| cache-downloads: true | |
| - name: Install snakePipes | |
| run: | | |
| micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv | |
| - name: pytest | |
| run: | | |
| micromamba activate snakePipes_CI | |
| snakePipes config --tempDir /tmp --condaEnvDir ./ | |
| pytest --verbosity=2 -rP tests/test_jobcounts.py |