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Funcotator in Mutect2 workflow lacks reference setting and fails to run

MattBMattB NewcastleMember ✭✭

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?


  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin
    edited February 2018

    I will pass this on as a bug to our workflows team. As this is one of our featured workspaces, we will certainly update the featured WDL ourselves to fix the bug if that ends up being the issue. Of course, if they have an easier non-WDL-changing fix, I'll be back to tell you what can be changed in the config.

  • MattBMattB NewcastleMember ✭✭

    Hi Kate, thanks let me know if they revise the WDL.

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