The pre-processing (alignment and ctf estimation) pipeline is defined as an apache airflow DAG. The code is at https://github.com/slaclab/cryoem-airflow/blob/master/dags/pipeline_single-particle_pre-processing.py
There are two main 'views' of the pipeline: from a per image workflow (graph) and from a global view of all images (tree)
Graph View
Tree View