Replace jupyter notebooks with scripts

[AshlinHarris]

Jupyter notebooks contain segmented python scripts with their outputs. Currently, they are used for many analysis steps for which simple scripts are better suited. Ideally, they should be reserved for plotting and quality control, and elsewhere replaced with scripts.

[aydemiro]

This is possible using the freebayes caller script instead of the jupyter route. We need to include it in the documentation. https://github.com/bailey-lab/MIPTools/blob/master/src/freebayes_caller.py

[arisp99]

A possible path forwards for this could be to take individual functions that are typically run from the jupyter notebook and package the functions into another container. For instance, we could make a new freebayes app that calls the freebayes caller script.

We could then generate apps for other commonly used functions like the vcf_to_tables function or the repool function.

[JeffAndBailey]

Note. we want both options. Notebook and script based method. Not mutually exclusive.