A quantum controller comprises a quantum control pulse generation circuit and digital signal management circuit. The quantum control pulse generation circuit is operable to generate a quantum control pulse which can be processed by any of a plurality of controlled circuits, and generate a first digital signal which can be routed to any of the plurality of controlled circuits. The digital signal management circuit is operable to detect, during runtime, to which one or more of the plurality of controlled circuits the first digital signal is to be routed, to manipulate the first digital signal based on the one or more of the plurality of controlled circuits to which the first digital signal is to be routed, where the manipulation results in one or more manipulated digital signals, and to route the one or more manipulated digital signals to one or more of the plurality of controlled circuits.