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.

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.

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.

Updated param files and remove_duplicates yaml & generator to successfully generator job.  Fixed a bug where workflow_job validation was crashing on non-string values.

Adjust the input format of the align.yaml module.  Fixed up minor issues across workflow job, module, and generator to get jobs correctly generating.

Fixed minor issues with job yaml files.  bowtie2 had wrong genome type specified.  Updated db_save_result to match new standard.