Scientific workflows are powerful tools for the management of scalable experiments, often composed of complex tasks running on distributed resources. Existing cyberinfrastructure provides components that can be utilized within repeatable workflows. However, data and computing advances continuously change the way scientific workflows get developed and executed, pushing the scientific activity to be more data-driven, heterogeneous, and collaborative. Workflow development today depends on the effective collaboration and communication of a cross-disciplinary team, not only with humans but also with analytical systems and infrastructure. This paper presents a collaboration-centered reference architecture to extend workflow systems with dynamic, predictable, and programmable interfaces to systems and infrastructure while bridging the exploratory and scalable activities in the scientific process. We present a conceptual design toward the development of methodologies and services for effective workflow-driven collaborations, namely the PPoDS methodology for collaborative workflow development and the SmartFlows Services for smart execution in a rapidly evolving cyberinfrastructure ecosystem.