Usage
As a user, you will mostly interface with the CUBI pipeline system using the snappy-snake
program.
This program is a wrapper around Snakemake and provides the following features:
a number of pre-packaged, well-tested workflows (pipeline steps) that are
driven by configuration and sample sheet files and
can be shared over multiple projects; and a
easy-to-use command line interface.
Here is how to get command line help:
$ snappy-snake --help