Modern science often requires the execution of large-scale, multi-stage simulation and data analysis pipelines to enable the study of complex systems. The amount of computation and data involved in these pipelines requires scalable workflow management systems that are able to reliably and efficiently coordinate and automate data movement and task execution on distributed computational resources: campus clusters, national cyberinfrastructures, and commercial and academic clouds. This paper describes the design, development and evolution of the Pegasus Workflow Management System, which maps abstract workflow descriptions onto distributed computing infrastructures. Pegasus has been used for more than twelve years by scientists in a wide variety of domains, including astronomy, seismology, bioinformatics, physics and others. This paper provides an integrated view of the Pegasus system, showing its capabilities that have been developed over time in response to application needs and to the evolution of the scientific computing platforms. The paper describes how Pegasus achieves reliable, scalable workflow execution across a wide variety of computing infrastructures. Comprehensive description of the Pegasus Workflow Management System.Detailed explanation of Pegasus workflow transformations.Data management in Pegasus.Earthquake science application example.