Is your feature request related to a problem? Please describe.

• There are separate steps for WGS & WES CNV calling, it should be unnecessary.
• The WGS branch has not kept up with progress in the rest of the pipeline
• It is a good playground to test new ideas for the overall pipeline architecture

Describe the solution you'd like

• Clear, easy to understand code
• Support for WES & WGS (& panel data?)
• Support for flat and panel of normals priors, as well as nromal/tumor pairs
• Support for cnvkit, purecn & sequenza (WES), cnvkit & possibly Control_FREEC for WGS
• Support for germline & somatic variants
• Support for purity (using ASCAT, Theta2/Hatchet or others)

Describe alternatives you've considered
Just updating somatic_wgs_cnv_calling.