Updated 3 things: 1st changed pepr arguments to be a list with a separator.  Updated argument parsing to allow joining list arguments with another value.  Updated conf to allow separator as a valid argument option.

Fixed incorrect argumnets in gem & peakranger.  Updated module_generator to use gfs_id for download script.

Small updates to many yaml files.  All peak callers now generating successfully.  Adjusted file_list input loding.  Fixed chip-job-ccat-format-bed to create correct number of columns.

Cleaned up peak call generator and yaml files to include default distribution arguments.  Removed gene annotation argument from peakranger.

Updated all yaml files to support type argument.  Heavily updated workflow_job parsing and verbosity.

Fixed reference to undefined variable key in workflow_module.  Adjusted param files to use bed arguments

Fixed minor issues in param yaml scripts. Updated workflow to add jobs and create relevant pegasus information.  Workflow can now generate download and alignment jobs, still needs testing.  Setup updated to include job-scripts.