Snakemake workflow: ngs-test-data
This workflow creates small test datasets for NGS data analyses. The generated data is available in the folders ref and reads, such that the repository can be directly used as a git submodule for continuous integration tests.
Authors
- Johannes Köster (@johanneskoester), https://koesterlab.github.io
Usage
Step 1: Install workflow
If you simply want to use this workflow, download and extract the latest release. If you intend to modify and further develop this workflow, fork this reposity. Please consider providing any generally applicable modifications via a pull request.
In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).
Step 2: Configure workflow
Configure the workflow according to your needs via editing the file config.yaml.
Step 3: Execute workflow
Test your configuration by performing a dry-run via
snakemake -n
Execute the workflow locally via
snakemake --cores $N
using $N cores or run it in a cluster environment via
snakemake --cluster qsub --jobs 100
or
snakemake --drmaa --jobs 100
See the Snakemake documentation for further details.