CWL: ensure HLA outputs in current work directory
CWL: ensure HLA outputs in current work directory

Do not write directly into staging directory since it is not shared
with the output process.

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