Fix for not generating bootstraps for single-end samples.
Fix for not generating bootstraps for single-end samples.

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