We describe the formal concept of a workflow to single-particle analysis of cryo-electron microscopy (cryo-EM) images in the RELION program. In this approach, the structure determination process is considered as a graph, where intermediate results in the form of images or metadata are the vertices, and different functionalities of the program are the edges. The new implementation automatically logs all user actions, facilitates file management and disk cleaning, and allows convenient browsing of a project's history. Moreover, new functionality to iteratively execute consecutive jobs allows on-the-fly image processing, which will lead to more efficient data acquisition by providing faster feedback on data quality. The possibility to exchange data processing procedures among users will contribute to the development of standardised image processing procedures, and hence increase accessibility for new users in this rapidly expanding field.