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bailey-lab / MIPTools

A suite of computational tools used for molecular inversion probe design, data processing, and analysis.
https://miptools.readthedocs.io
MIT License
6 stars 9 forks source link

Replace jupyter notebooks with scripts #16

Open AshlinHarris opened 2 years ago

AshlinHarris commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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