Question on -r argument of DataProcessingPipeline

[royalchan]

Hi All,

I am trying to use the DataProcessingPipeline.scala with GATK Queue.jar and it doesn't seem to recognize the -r argument (which, by instruction, should be mandatory and provide information of the "path to R resources folder inside the Sting repository"). I always got the error "##### ERROR MESSAGE: Argument with name 'r' isn't defined."

Could any one help please? Thanks!

Best,
RC

[RDW]

Looking at the current pipeline scala script itself, path_to_r is no longer a required (or optional) parameter (it's there as 'required' in older versions). Maybe they've dropped this dependency without updating the docs?

[royalchan]

Thanks RDW! It looks like so.

Thanks RDW! It looks like so. but still no solutions yet . It seems still to be required but can't be fulfilled without getting the argument recognized.