CWL: create secondary files for aligner indices
CWL: create secondary files for aligner indices

Avoids problems with missing indices during current test docker runs.

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