Use separated boolean parameters for vep and exomiser - HIGH PRIORITY

[LysianeBouchard]

Description of feature

A user can enable vep / exomiser via the --tools parameter. We would like to replace this option by 2 separated boolean options (ex: --with-vep --with-exomiser).

We think that it will reduce the complexity of the code, as, with the tools parameter, we need to add extra logic to parse the value. With dedicated boolean parameters, the logic to determine whether or not vep/exomiser applies is more straightforward and easier to read in the code.

Using high priority as, ideally, we would like to do it before qlin deployment since there is a breaking change in the input/output interface. Such change will be harder to do when we have a pipeline deployed in production.