ensemble: limit effects cleaning to annotated VCFs
ensemble: limit effects cleaning to annotated VCFs

Avoids issues with empty or `effects: false` input VCFs.

Thanks to Ivan De Dios
https://groups.google.com/d/msgid/biovalidation/fb4bbf96-4c1f-4d34-9a9c-73e966439276%40googlegroups.com.

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