Expose more parameters of tools

[a-frantz]

In the early days of this repo we tended to only expose parameters we use. We've since gotten much better at exposing parameters as we add tools. But there are still many old tasks with very little parameterization.

[a-frantz]

There are few places where we (me and @adthrasher ) decided it was best not to expose specific parameters. The reasoning here is varied, but is generally along the lines of "making use of this parameter would violate a best practice". These cases are sometimes documented (https://github.com/stjudecloud/workflows/blob/main/tools/qualimap.wdl#L7) but there are definitely some "ghost" omissions. I believe in STAR and Kraken both, perhaps in other tools as well.

We should correct this with a dedicated key in the meta section. Do not have a specific key to propose at this time.

[Gyan-max]

Hi @a-frantz can i work on this issue?