The execution of the workflow is superficially no different from the execution of workflows that use purely local entities, but some changes do occur.

The registered or known input files are now uploaded for each design and loaded onto the server to make the remote process executable. The remote process also needs all the components referenced in the defined script to be used and eventually to run. This means that defined program calls must be able to be executed on the server. This also includes their dependencies, such as the potential non-existence of a graphical desktop environment.