UMI prep: document autopair; single core args
UMI prep: document autopair; single core args

- Document R1/R2/R3 naming for autopair
- Allow specification of core usage for single runs

Fixes #2123

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