First commit! #1
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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@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - 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 singularity sra-tools | |
| - name: Download example data | |
| run: | | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR969/008/SRR9697628/SRR9697628_1.fastq.gz -O test_data/SRR9697628_1.fastq.gz | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR969/008/SRR9697628/SRR9697628_2.fastq.gz -O test_data/SRR9697628_2.fastq.gz | |
| - run: echo "Finish installing snakemake" | |
| - name: Run snakemake | |
| run: | | |
| snakemake --use-singularity --use-conda --cores 4 |