CWL: avoid unconnected input variables
CWL: avoid unconnected input variables

Only include input variables in workflow that get used downstream.
Avoids confusing unconnected inputs and need to manage them. Help
with DNAnexus support. Thanks to @geetduggal

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