@tvparys, you don't call cleaning methods for cytoscape input, right? In that case you need to have cleanInput=true when calling project.addRunConfiguration from CyProject (fixed it for you, this is just a note). If you would call NetworkCleaning methods yourself, put the parameter to false to avoid redundany (+ more time). But I think the first option is the better one.
@tvparys, you don't call cleaning methods for cytoscape input, right? In that case you need to have
cleanInput=truewhen callingproject.addRunConfigurationfromCyProject(fixed it for you, this is just a note). If you would callNetworkCleaningmethods yourself, put the parameter to false to avoid redundany (+ more time). But I think the first option is the better one.