CWL: version pins and updated tools
CWL: version pins and updated tools

Remove gatk-framework and pin tools required for version conflicts,
mirroring fixes in cloudbiolinux.

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