Qualimap: avoid double files in output
Qualimap: avoid double files in output

Double supplied `genome_results.txt` file in both base and secondary
confuses some CWL analysis engines because of staging the same file
twice. @vladsaveliev -- let me know if this breaks anything.

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