Custom workflows

Creating custom workflows and graphs encapsulating common behaviour can be done by adding modules to the maize/graphs namespace. Create an appropriate file and define your graphs as described in the user guide. For workflows usable from the commandline, define your workflow inside a function taking no parameters and no return (see the user guide on workflows) and call maize.utilities.io.setup_workflow() with your defined workflow. This will instantiate a commandline parser and expose all workflow parameters as arguments and flags. To make it callable anywhere, add this function to setup.cfg.