Closed-loop neuromodulation control systems facilitate regulating abnormal physiological processes by recording neurophysiological activities and modifying those activities through feedback loops. Designing such systems will require closed-loop workflows with interoperable modules. Workflow frameworks enable standard modular designs, offering reproducible automated pipelines. But workflow languages and standards limit their aim to executions represented by directed acyclic graphs (DAGs). DAGs require a pre-defined start and end execution step with no cycles, thus preventing the researchers from using the standard workflow languages as-is for neuromodulation control systems which consist of closed-loops. Testing and prototyping closed-loop neuromodulation control systems require in-silico simulations before being integrated into in-vivo experimental setups. In this paper, we present NEXUS, our workflow orchestration framework for distributed analytics systems. NEXUS proposes a Software-Defined Workflows approach, inspired by Software-Defined Networking (SDN), which separates the data flows across the service instances from the control flows. NEXUS enables creating interoperable workflows with closed loops by dynamically defining the workflows in a logically centralized approach, from microservices representing each execution step. The centralized orchestrator of NEXUS facilitates dynamically composing scientific workflows from the service nodes with minimal restrictions. NEXUS further supports composing and managing complex workflows from existing workflows via its orchestrator by representing the workflows as directed hypergraphs (DHGs) rather than DAGs. We build sample workflows for a few closed-loop neuromodulation control systems with NEXUS. We illustrate a seamless execution of neuromodulation control systems by supporting loops in a workflow as the use case of NEXUS. Our evaluations highlight the feasibility, flexibility, performance, and scalability of NEXUS in modeling and executing workflows with closed-loops.