We describe a reusable architecture and implementation framework for managing science processing pipelines for mission ground data systems. Our system, dubbed ``PCS'', for Process Control System, improves upon an existing software component, the OODT Catalog and Archive (CAS), which has already supported the QuikSCAT, SeaWinds and AMT earth science missions. This paper focuses on PCS within the context of two current earth science missions: the Orbiting Carbon Observatory (OCO), and NPP Sounder PEATE projects.