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