Major refactor pipelines

[JoeZiminski]

This PR refactors all pipelines to use classes for flexibility.

1. This is done for preprocessing but deeper refactorings and tidyups to preprocessing should be made. It will be good to split out pp functions and the pp pipeline class
2. Then do for sorting and post-processing in the same form.
3. Finally do for the main pipeline.

This isn't actually going to be as much work as thought, submitit works really nicely just passing the class!