Motivated by the widespread use of workflow systems in e-Science applications, this article introduces a formal analysis framework for the verification and profiling of the control flow aspects of scientific workflows. The framework relies on process algebras that characterise each workflow component with a process behaviour, which is then used to build a CTL state model that can be reasoned about. We demonstrate the benefits of the approach by modelling the control flow behaviour of the Discovery Net system, one of the earliest workflow-based e-Science systems, and present how some key properties of workflows and individual service utilisation can be queried at design time. Our approach is generic and can be applied easily to modelling workflows developed in any other system. It also provides a formal basis for the comparison of control aspects of e-Science workflow systems and a design method for future systems.