Cloud computing is an emerging computing paradigm that can offer unprecedented scalability and resources on demand, and is getting more and more adoption in the science community, while scientific workflow management systems provide essential support such as management of data and task dependencies, job scheduling and execution, provenance tracking, etc., to scientific computing. As we are entering into a "big data" era, it is imperative to migrate scientific workflow management systems into the Cloud to manage the ever increasing data scale and analysis complexity. We propose a reference service framework for integrating scientific workflow management systems into various Cloud platforms, which consists of eight major components, including Cloud workflow management service, Cloud resource manager, etc., and 6 interfaces between them. We also present a reference framework for the implementation of Cloud Resource Manager, which is responsible for the provisioning and management of virtual resources in the Cloud. We discuss our implementation of the framework by integrating the Swift scientific workflow management system with the OpenNebula and Eucalyptus Cloud platforms, and demonstrate the capability of the solution using a NASA MODIS image processing workflow and a production deployment on the Science@Guoshi network with support for the Montage image mosaic workflow.