feat!: 237 revive cnvkit

[ericblanc20]

• Extends the panel_of_normals step to create a cnvkit reference based on exome of wgs normal samples
• Updates & extends the cnvkit tool for the somatic_targeted_seq_cnv_calling.
• Allows cnvkit as tool for the somatic_wgs_cnv_calling step

Note that the changes break the plots creation for the control_freec tool in the somatic_wgs_cnv_calling step. Following a discussion with Manuel, this step will need to be refurbished anyway, and possibly merged with the somatic_targeted_seq_cnv_calling step, which performs the same function for exome data.

[Nicolai-vKuegelgen]

I don't see anything glaring, so overall lgtm.
However, keep in mind that I'm not overly familiar with these tools, and I didn't specifically check that the snappy/snakemake changes all work out.

[coveralls]

Coverage: 85.037% (+0.4%) from 84.613% when pulling cae427d on 237-revive-cnvkit into 5ecad1a on main.