Allow for the pipeline to run on reference genomes with more than one contig

Currently the pipeline is focused on running on a organisms with a single chromosome and no additional plasmids. In order to support multiple contigs a substantial overhaul will be needed. However, this is the highest priority feature needed to be implemented.

Some things that need to be reworked to make this possible:

[x] Custom python code dealing with median normalization
[x] CMARRT algorithm for peak calling
[x] Updating all deeptools calls to allow for multiple contigs
[x] Interface for specifying the reference genome in the config/config.yaml file

mikewolfe / ChIPseq_pipeline

Allow for the pipeline to run on reference genomes with more than one contig #5