A fluid processing system, comprising: a first separation device; a second separation device; an electroporation device (118, 120); a pump assembly including a plurality of pumps (P1-P6); and a controller configured to actuate the pump assembly to convey blood from a blood source into the first separation device, actuate the first separation device to separate a mononuclear cell product from the blood, actuate the pump assembly to convey at least a portion of the mononuclear cell product into the electroporation device (118, 120) to modify a genome of at least one of the cells of the mononuclear cell product, and actuate the pump assembly to convey at least a portion of the modified mononuclear cell product to the blood source, wherein the second separation device is configured to wash the mononuclear cell product and to wash the modified mononuclear cell product, and the controller is configured to selectively control the second separation device during a first version of a mononuclear cell processing procedure to wash the mononuclear cell product, to control the second separation device during a second version of the mononuclear cell processing procedure to wash the modified mononuclear cell product, and to control the second separation device during a third version of the mononuclear cell processing procedure to wash neither the mononuclear cell product nor the modified mononuclear cell product. a first separation device; a second separation device; an electroporation device (118, 120); a pump assembly including a plurality of pumps (P1-P6); and a controller configured to actuate the pump assembly to convey blood from a blood source into the first separation device, actuate the first separation device to separate a mononuclear cell product from the blood, actuate the pump assembly to convey at least a portion of the mononuclear cell product into the electroporation device (118, 120) to modify a genome of at least one of the cells of the mononuclear cell product, and actuate the pump assembly to convey at least a portion of the modified mononuclear cell product to the blood source, wherein the second separation device is configured to wash the mononuclear cell product and to wash the modified mononuclear cell product, and the controller is configured to selectively control the second separation device during a first version of a mononuclear cell processing procedure to wash the mononuclear cell product, to control the second separation device during a second version of the mononuclear cell processing procedure to wash the modified mononuclear cell product, and to control the second separation device during a third version of the mononuclear cell processing procedure to wash neither the mononuclear cell product nor the modified mononuclear cell product. actuate the pump assembly to convey blood from a blood source into the first separation device, actuate the first separation device to separate a mononuclear cell product from the blood, actuate the pump assembly to convey at least a portion of the mononuclear cell product into the electroporation device (118, 120) to modify a genome of at least one of the cells of the mononuclear cell product, and actuate the pump assembly to convey at least a portion of the modified mononuclear cell product to the blood source, wherein the second separation device is configured to wash the mononuclear cell product and to wash the modified mononuclear cell product, and the controller is configured to selectively control the second separation device during a first version of a mononuclear cell processing procedure to wash the mononuclear cell product, to control the second separation device during a second version of the mononuclear cell processing procedure to wash the modified mononuclear cell product, and to control the second separation device during a third version of the mononuclear cell processing procedure to wash neither the mononuclear cell product nor the modified mononuclear cell product.