Update RNA-seq template with inline options.
Update RNA-seq template with inline options.

Thanks to @skanwal for pointing out this is confusing for
onboarding new users.

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