CWL: fix assignment of VCF/BAMs to samples
CWL: fix assignment of VCF/BAMs to samples

Ensure we iterate though all choices for misassigned input BAMs and VCFs.

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