add depth to our test coverage

[a-frantz]

We have 100% tool test coverage which is awesome! But most of our tools lack sufficient test depth, as in advanced options aren't being checked.

An example:
The STAR tests currently only test with a single pair of FASTQs (and therefore only one Read Group), though the logic for the task has some potential pitfalls when multiple pairs/RGs are supplied that we do not currently test.