Adding parameter to specify reference file name in nextflow implementation

[srcrowl]

Is your feature request related to a problem? Please describe.

Currently, the nextflow implementation of KSTAR expects a specific file name for the reference file ('Human_PhosphoProteome_mapped_annotated_02_26_20.csv') which is not what is downloaded by config.install_resource_files(), which may lead to confusion or difficulties running, especially as it is not easily diagnosed. Currently, the way this file is provided to nextflow is to indicate the directory containing the files, but not the exact file name. This will be problematic especially as we start updating the reference file for future iterations of KSTAR

Describe the solution you'd like
Instead of the current setup, it include a resource_file_name parameter (include a default that is what is downloaded by KSTAR automatically). I also suggest, although this is less critical, changing the network_dir parameter to not be relative to the resource directory, as this has also caused some confusion at times.