Reorganize config and rename ambiguous params

[jashapiro]

The section nextflow.config with index file locations is getting pretty big, and with multiple indices, some of the parameter names are getting a bit ambiguous. For example, fasta and gtf should probably be something like ref_fasta and ref_gtf. Changing these will require changing their use throughout the modules.

We can also reorganize somewhat, breaking up the config file into smaller ones that define the processes and parameters separately and taking advantage of the includeConfig directive. I also realized that we can use variables in the config files , so we can cut a lot of redundant path info. More info on this here: https://www.nextflow.io/docs/latest/config.html?highlight=configuration#config-syntax