CWL: avoid creating final and inputs directories during generation
CWL: avoid creating final and inputs directories during generation

Avoids non-used directories when preparing configuration. Thanks to @ohofmann

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