RNA STAR allows job submission when required inputs are missing, results in obscure cluster error

[jennaj]

The option "Count number of reads per gene" can be set to "Yes" with the option "Gene model (gff3,gtf) file for splice junctions" left without a selected ref anno dataset OR with the option "Reference genome with or without an annotation" set an index without built-in annotation.

"Yes" for the count function is internally dependent on the inclusion of reference annotation from one of these two sources.

When this usage problem occurs, it results in a job failure that is difficult for end users to troubleshoot.

It would be better if the input dependency was trapped and the user was warned at job submission that there are missing required inputs. Tools do this in different ways - but most will highlight the missing input with help text to guide in proper usage.

If we do that, will avoid the job from even being able to be submitted before the inputs are correct and in sync.

Does this PR and others related to the upgraded tool capture this usage issue? Should/could it be added before the MTS is updated? Or possibly at the next update if too late now?
#1726

ping @bgruening