Add command parameter groups

[leexgh]

We have more and more parameters now that are a bit hard to track, the idea is to create a few groups for command parameters:
for example:

--minimal activate minimal set of annotation columns
--full add all available annotation columns
--debug add all available annotation columns, and need to specify the log file and error report file, can also extend to different levels of logging (https://github.com/genome-nexus/genome-nexus-annotation-pipeline/issues/247)