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.
- Johannes Köster (@johanneskoester), https://koesterlab.github.io
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).
Configure the workflow according to your needs via editing the file config.yaml.
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.
This workflow uses resources from the EMBL-EBI Ensembl Biomart and the Ensembl FTP downloads. Neither of these resources seems to have explicit licensing information mentioned, so the general EMBL-EBI licensing suggests that the EMBL-EBI Terms of Use apply, with no restrictions on re-use.
Additionally, data from the E-GEUV-1 ArrayExpress / BioStudy is used.
As no License field is included for this dataset, it also defaults to the EMBL-EBI Terms of Use according to the BioStudies Help/FAQ.