PROVENANCE:skip manifest file if it is empty
PROVENANCE:skip manifest file if it is empty

cc: da39a3ee5e6b4b0d3255bfef95601890afd80709@chapmanb, We removed gatk from toolplus-packages.yaml (it was empty),
and bcbio gives an error because it tries to iterate through a NoneType
object. I hope this doesn't affect anything else.

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