Updates M2 WDLs to 1.0 and fixes NIO #6108
Conversation
| String? realignment_extra_args | ||
| Boolean? run_orientation_bias_mixture_model_filter | ||
| input { | ||
| File? intervals |
There was a problem hiding this comment.
The comment
# Mutect2 inputs
got lost. Could you put that back in please.
|
@meganshand Just one minor thing. |
|
Does these wdl scripts are OK for local running with cromwell-44 and gatk4.1.2.0? Since, in this repo: gatk-workflows/gatk4-somatic-snvs-indels. Broad also provided 1 Mutect2.wdl script. I am wondering which one is the newer and better for local run? I am trying to find Mutect2.wdl and Mutect2_pon.wdl scripts which are suitable for local running. |
|
@GitHub-Fish These WDLs should work locally as well as in the cloud. If you're using gatk version 4.1.2.0 you might want to use that version of the WDLs as well (I didn't make any functional changes in this PR but it's possible that there have been some). Also if you have a question about gatk-workflows, I'd recommend asking on the gatk forum. They'll be able to answer better about the versions in that repo. |
I haven't tested these in Terra (or in the cloud at all). But the local tests should now be passing. Happy to test this in Terra if there's an easy way to do that. @davidbenjamin or @fleharty care to review?