align prep: correctly handle single sample inputs
align prep: correctly handle single sample inputs

Fixes bug in addition of multiple input support for the standard bgzip case.
Fixes #2492

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