Add Matthias's cromwell fix.
Add Matthias's cromwell fix.

lbeltrame/bcbio-nextgen,vladsaveliev/bcbio-nextgen,a113n/bcbio-nextgen,a113n/bcbio-nextgen,a113n/bcbio-nextgen,vladsaveliev/bcbio-nextgen,chapmanb/bcbio-nextgen,chapmanb/bcbio-nextgen,chapmanb/bcbio-nextgen,lbeltrame/bcbio-nextgen,vladsaveliev/bcbio-nextgen,lbeltrame/bcbio-nextgen