RatGTEx pipeline v1

This is the pipeline used to process data for the RatGTEx Portal. It is loosely based on the GTEx eQTL mapping pipeline, though it includes some utility scripts from there in their entirety. All code for this pipeline can be found in the repository. It is built on Snakemake, a Python-based framework for reproducible data analysis. The commands reproduced here use Snakemake-style templating, with variables in brackets to represent different input/output file names and parameters.