Aloha. I am using GATK in Galaxy for the first time, on a local Galaxy server, and when I try to run Count Covariates I get the error: ERROR stack trace org.broadinstitute.sting.commandline.InvalidArgumentException: Argument with name 'T' isn't defined. at org.broadinstitute.s
I have looked at the GATK Count Covariates command line, and it looks to me like the argument with name 'T' is not a place where I need to input a file, but is where the Count Covariates software information goes. I get this same error when trying to run Realigner Target Creator. I wondered if this might be something that could be simply fixed by reinstalling the wrappers for GATK, or something along those lines? Thank you!
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