Fixed rewrite logic in _add_module.  Added check for download_from_gridfs to avoid adding multiple download jobs for the same file.

Added granularity over rewrite for each individual module.  Align and remove_duplicate default to the workflow value, peak call defaults to false.

Enhanced workflow functionality to only remove unused jobs.  Potentially could have removed a job that was being used as a dependant.

Change argument to string in download_From_gridfs params to match job file.  Created outputs and added jobs to dax.  When using download from gridfs, remove unnecessary jobs from the dax.

Fixed database query to correctly reflect if sample arrays are empty.  Return actual document instead of truthy value. Added output file name and timestamp to save_results.: