CWL: remove old commandline serialization code
CWL: remove old commandline serialization code

Removes hacks for supporting multiple samples, instead parsing from
JSON serialized inputs.

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