Installation

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 repository. Please consider providing any generally applicable modifications via a pull request.

To be able to run the workflow, you at least need to have snakemake and pandas installed. A basic (conda) environment containing these dependencies can be setup as follows:

conda create -n snakemake snakemake pandas

The various external tools (e.g. bwa, samtools) are managed automatically by snakemake if the --use-conda flag is used. Otherwise, these external tools also need to be installed into the environment or must be available in $PATH.