Turn on quiet mode during Cufflinks assembly.
Turn on quiet mode during Cufflinks assembly.

Closes #2361. Thanks to @hilu2016 for pointing out the oversight.

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