Removed code that enters default filtering options when none are specified because these options will be set explicitly at job submission and also we need the ability to run this stage with no filtering options which the current configuration would not allow.
Removed code that enters default filtering options when none are specified because these options will be set explicitly at job submission and also we need the ability to run this stage with no filtering options which the current configuration would not allow.

wgerlach/pipeline,MG-RAST/pipeline,wgerlach/pipeline,teharrison/pipeline,teharrison/pipeline,wgerlach/pipeline,MG-RAST/pipeline,teharrison/pipeline,MG-RAST/pipeline