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.

Updated workflow module parsing to support new format.  Argument types are now loaded from workflow_job data instead of being repeated within the module itself.

Updated workflow_job to use internal type values for arguments instead of passed ones.  No longer need types included in workflow_module.

Removed unnecessary print statement.  Added optionally argument loading.  Fixed valid workflow generation test.

Job argumnet creation is now actually legible AND works with the new style of inputs/outputs as well as job definition files.