Almost every step that can be accomplished using the user interface can also be accomplished using a pipeline command - the pipeline is essentially a set of commands/functions that allow you to streamline your data processing and reproducible for other subjects.
It's always recommended to learn the manual steps PRIOR to writing a pipeline command - learning the interface will help you build your pipeline.
When writing a pipeline to build a CMZ file, your script should follow the general procedure outlined below.
Notes: