starix and pytest in same job #7
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 | |
| - 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 |