Fixed a validation error with jobs with non-required arguments.  Trying to evaluate numeric types without a value.

Fixed arguments for pepr peak calling.  Updated params in peak_call module to correctly reflect the output files produced by hidden domains.

Resolve "MongoDB auth should be optional"

Closes #34

See merge request !33

Heavily updated the yaml file parsing for two primary reasons:
1. Make it more understandable what's actually going on underneath.
2. Allow for optional arguments.

Bridges compatability

Updates so things work on bridges as well as on local submit sites.

See merge request !32

Added option to prevent saving files to database.  Updated generator handling of save_db & rewrite arguments.  Minor style fixes & comment updates.  Chip-gen now supports --save-db option.

Updated file interpolation to use literal name instead of object.  This will make some edge case parsing easier in the future.

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 command in music_puncatte.  Added print statement when skipping jobs in module_generator.

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