Data from complex modern astronomical instruments often consist of a large number of different science and calibration files, and their reduction requires a variety of software tools. The execution chain of the tools represents a complex workflow that needs to be tuned and supervised, often by individual researchers that are not necessarily experts for any specific instrument. The efficiency of data reduction can be improved by using automatic workflows to organise data and execute a sequence of data reduction steps. To realize such efficiency gains, we designed a system that allows intuitive representation, execution and modification of the data reduction workflow, and has facilities for inspection and interaction with the data. Reflex includes novel concepts to increase the efficiency of astronomical data processing. While Reflex is a specific implementation of astronomical scientific workflows within the Kepler workflow engine, the overall design choices and methods can also be applied to other environments for running automated science workflows.