We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
joint-discovery-gatk4-local.wdl uses deprecated output syntax
In the GitHub-provided, official WDL files for running GATK, the "local" version of joint discovery uses a deprecated form of declaring outputs, which prevents it from being run as a subworkflow.
Note that another user already has a pull request with a fix for this issue. However, that has been pending for nearly a month now, so might be worth accepting: