test boh #56
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| name: Testing | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| workflow_dispatch: | |
| jobs: | |
| Testing: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: | | |
| conda install -c conda-forge mamba | |
| - name: Setup snakemake | |
| run: | | |
| mamba install -c conda-forge -c bioconda snakemake | |
| - run: echo "Finish installing snakemake" | |
| - name: Download files with wget | |
| run: | | |
| wget -O test_data/gencode.v46.primary_assembly.basic.annotation.gtf.gz https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_46/gencode.v46.primary_assembly.basic.annotation.gtf.gz | |
| wget -O test_data/GRCh38.primary_assembly.genome.fa.gz https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_46/GRCh38.primary_assembly.genome.fa.gz | |
| - name: Run snakemake | |
| run: snakemake -s workflow/snakefile_final.smk --use-conda --rerun-incomplete --core 2 -k | |