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Grid computing technique is a mature technique for distributed-data computing and processing. Scientific workflow (SWF) technique is one of the most important parts of grid computing and typically used for job scheduling, distributed services invocation and distributed data processing. However, rare previous literatures studied the security issues of SWF in the design of scientific workflow though it is important in the implementation. In this paper, we make a deep analysis on the frameworks of SWF, discuss the potential safety hazard and present the possible security vulnerabilities in the SWF technique. We then propose the solutions to solve the current security issues. Finally, we discuss the future work on confidential communication and data exchange in SWF.