Xenomake

==============

MAJOR CHANGES:
The major change to this project is the introduction of the pip package xenomake.
All calls made through xenomake package on command line.
This minimizes the amount of configuration and specification of absolute file paths.
We no longer require you to download this repository

MINOR IMPROVEMENTS:
- Downloading of genomes, star indices, and xengsort index available through cli
- More robust error detection in project configuration stage to minimize amount of snakemake re-execution
- xengsort included as conda install

ADDITIONAL FUNCTIONALITIES:
- updated config file to better organize variables by variable type
- added spatial modes for dbit-seq, visium, and seq-scope
- added run mode arguments to customize how reads are handled in run
- added config option to customize run_mode arguments and spatial_mode arguments

Updated scripts to handle v2 of xengsort
Updated config.py and species_parser.py files
Fixed bugs relating to index generation
Uploaded a downsampled test dataset
Added Exceptions to species_parser.py and config.py to ensure correct file inputs
Fixes bug that can be thrown by snakemake pipe() argument

Improved on read overlap funcitons
Reduced number of I/O operations
Provided optional downstream spatial processing
Made filtering ambiguous/both reads optional
Converted hdf5 generation to python in order to reduce dependencies
Created Log and QC directories/outputs

Completed Pipeline for PDX Spatial Processing
Further edits will include functionality for single cell projects and other spatial chemisty

First Implementation of Visium PDX Processing Pipeline
Currently no implementation for chemistry outside of Visium v2, look to future releases for more customization