To make the pipeline more robust, the global python variables for
various settings were removed where possible. Their values have been
moved to the configuration json file, and a jsonschema validation has
been added to the pipeline to make sure the configuration is valid.

The downsampling step using seqtk has been remove since it was not used.

The following additional changes were made:
 - Remove all --config values except CONFIG_JSON
 - Extend the config schema with the required and optional files that
   are supported
 - Add jsonschema validation of CONFIG_JSON
 - Remove global variables for scripts, add them to settings
   dictionary
 - Remove global variable for SAMPLES, use the settings dictionary
   instead
 - Remove support for multiple bed files
 - Remove support for multiple refFlat files
 - Remove support for downsampling of reads
 - Add json and jsonschema to the requirements
 - Update tests to work with the new config file