Recent research efforts have yielded significant advancements in manipulating objects under homogeneous settings where the robot is required to either manipulate rigid or deformable (soft) objects. However, the manipulation under heterogeneous setups that involve both deformable and rigid objects remains an unexplored area of research. Such setups are common in various scenarios that involve the transportation of heavy objects via ropes, e.g., on factory floors, at disaster sites, and in forestry. To address this challenge, we introduce DeRi-Bot, the first framework that enables the collaborative manipulation of rigid objects with deformable objects. Our framework comprises an Action Prediction Network (APN) and a Configuration Prediction Network (CPN) to model the complex pattern and stochasticity of soft-rigid body systems. We demonstrate the effectiveness of DeRi-Bot in moving rigid objects to a target position with ropes connected to robotic arms. Furthermore, DeRi-Bot is a distributive method that can accommodate an arbitrary number of robots or human partners without reconfiguration or retraining. We evaluate our framework in both simulated and real-world environments and show that it achieves promising results with strong generalization across different types of objects and multi-agent settings, including human-robot collaboration.