CWL: avoid bai/tbi indices if not present
CWL: avoid bai/tbi indices if not present

Generalizes lookup of secondary file existence and only add to CWL
when present. Includes lookups for both bai and tbi indices which
were previous assumed. Thanks to @tfmorris

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