CWL: prepare in-place VCF files, before adding to inputs
CWL: prepare in-place VCF files, before adding to inputs

Avoids relative path errors when working with pre-prepared VCF inputs that
don't need extra processing.

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