Hi, I've just run a clone of the Somatic-SNVs-Indels-GATK4 workspace with run Funcotator set to true. It appears to have failed, looking at the standard error output it would appear that the WDL / method config is missing a reference version argument which should be passed to Funcotator:
A USER ERROR has occurred: Argument ref-version has a bad value: NO_REFERENCE_VERSION_GIVEN. 'NO_REFERENCE_VERSION_GIVEN' is not a valid value for ReferenceVersionType. Possible values: {hg19, hg38}
Within firecloud the error has been trapped as Failed to delocalize files: failed to copy the following files:<gs path gubbins>/SM-74P4M-funcotated.vcf.idx - I'm guessing this is the error when no output is produced to copy back to the gs bucket.
You might want to update the WDL and method config to expose a setting for this. I trust there is a way of adding arbitrary command-line arguments to a methods configuration, I assume this will also require changes in the WDL?