feat: Generalize mutect2 wrapper

[tedil]

This PR generalizes / combines the mutect2/run and mutect2/prepare_panel wrappers, such that the code is the same but logic can be controlled via snakemake inputs and params (e.g. whether to call tumor/normal or normal only).

TODO

• config → params treatment
• adapt calling code of mutect2/run and mutect2/prepare_panel

[ericblanc20]

Quick question: the java_options are taken from the config at the moment. But shouldn't they be taken from the snakemake resources? As far as I understand, you eventually want to put all resources allocation under functions in __init__.py code (which may read the configuration before passing the final resources to snakemake, of course). Is that the plan?

And another question/remark: I notice that you explicitly assign each argument/parameter to a separate value (for example

if germline_resource := config.get("germline_resource"):
    germline_resource_param = f'--germline-resource {germline_resource}'
else:
    germline_resource_param = ""

I like it, the code is nice and clean. I haven't done that in recent branches, based on the fact that I was concerned by the explosion of parameters in some wrappers. Should I reconsider?

[tedil]

java_options is something we have to consider "globally" for snappy, not only here. I think they could potentially be derived from the resources (as for example Xmx is constrained by the memory resource) as params.

As for the separate values: I mainly do this for optional parameters. A utility function such as build_parameter(args, arg_name, cmd_option) would make it a little bit shorter/less repetitive, e.g. optional_parameter(args, "germline_resource", "--germline-resource"). (Perhaps with a better name.)