It seems resaving the workflow to create the attached workflow (to overcome path issues with pauls nested workflows) fixes the above problem. However, the workflow still doesn't complete for other reasons - yet to be determined.
The problem reported here still remains an issue though and I'll attach the original workflows. The outer workflow is pauls_workflow.xml and the inner nested workflow is pauls_workflow-inner.xml . The outer workflow scufl will need editing to correct the path to the inner workflow, which is currently set to:
<s:workflow>
<s:xscufllocation>file:/Users/sowen/tmp/pauls_workflow-inner.xml</s:xscufllocation>
</s:workflow>
an example input is "african trypanosomiasis AND mouse" (without the quotes)