Existing workflow managers, such as Biovia's PipelinePilot or KNIME, are commonly used to automate such tasks in a more standardized way. However, they have certain limitations that led us to develop a new solution, specifically, we required a tool that would seamlessly integrate with our deep learning based molecular de novo design tool, REINVENT, to construct complex scoring components through vendor agnostic workflows while being flexible enough to support rapid prototyping. Here we present Icolos, a modular, flexible and extensible workflow manager that provides a unified interface to a host of common commercial and opensource computational packages, encompassing docking, molecular dynamics, binding free energy and quantum mechanical calculations. Icolos has built-in REINVENT integration and has been used in-house both to incorporate complex structural calculations into the agent's feedback loop, and as a standalone workflow manager for post-processing results. We achieve efficient scaling through parallelisation of computationally demanding calculations and performance in agreement with manually executed workflows, often at a fraction of the runtime of previous implementations relying on shell scripts or submission from a GUI.