Create config file for pipeline to gather input information

[slsevilla]

Problem:

• Currently the pipeline requires several inputs from the command line, including full paths to reference files.

Solution

• To avoid mistakes and to ease use, a config file will be used to take in parameters

[slsevilla]

Config file should include (to be updated):

• input fastq location
• species
• reference files

Run executable with:

• output_dir location

[kelly-sovacool]

This could be used to implement #29 -- e.g. any user-given config options that match the default/template config would override the default.