I am continueing to struggle with the API....

I have created a workflow execution engine that submits a workflow using the examples in the API (scripts/api).

When I run the WF on data in the LIBRARIES everything works fine.

But when I choose a HISTORY as my source of data, the WF executes fine, but the history I use is emptied of all the files in there!

This is very bizarre....Any ideas what is going on here?

I know not a lot of people are using the API, but it is the only way I can run paired end WF on more than a couple of samples...