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Small updates to JointVcfFiltering WDL #8027
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I gave this a default, but I can also see an argument for having it be a required input since it's somewhat tied to the input annotations (which are currently required). Would love a second opinion.
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Good point. I think it makes sense to make it required.
More generally, for task-level required/optional arguments, I like the style we use in the CNV WDLs. That is, all arguments are exposed, and optional arguments have their defaults specified in the command line rather than in the parameter block (see e.g.
gatk/scripts/cnv_wdl/cnv_common_tasks.wdl
Line 34 in ef50c08
Not sure if this is the way automatic WDL generation works (haven't tried it myself), but I think it makes sense. And ideally we'd be good about using that functionality that to keep the defaults in sync between the WDL and the jar. Baby steps!
Don't worry about all that for this PR---I'll tackle it in my push. Thanks!
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Ah makes sense, it does seem cleaner to keep the defaults in the command line.