How HoCoRT works
When HoCoRT is initially run, it runs the default user interface located in interface.py. If a pipeline is chosen, the interface will create an instance of it and run it. The pipelines use pre-implemented tool classes. These classes use execute.py to spawn and execute subprocesses on the OS level.
Pipelines are built such that they may combine multiple existing tools such as aligners to process the input data. Combining multiple tools gives the developers of the pipelines more freedom to build pipelines which focus on different aspects of processing, for example, they may focus on sensitivity or speed.