Try Taverna plugin is very likely an answer to automation of bioinformatics workflows...
The Taverna Interaction Service: enabling manual interaction in workflows by Anders Lanzén and Tom Oinn
Taverna is an application that eases the integration of tools and databases for life science research by the construction of workflows. The Taverna Interaction Service extends the functionality of Taverna by defining human interaction within a workflow and acting as a mediation layer between the automated workflow engine and one or more users.
(Bioinformatics Advance Access abstract)