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.:

Name the metadata yaml files to using the full filename
and extension of the corresponding workflow output file.
This is needed to avoid name collisions between yaml files
in the same module.