I find it would be a desirable feature to have on Terra, for users to be able to configure cromwell in a custom way for specific workflows. The default configuration may not perfectly suit for all users and workflows. A concrete use case is to be able to specify workflow options such that multiple job outputs can be put into a flattened output directory, as discussed in these relevant threads:
It probably is not a good idea to expose all configuration options to users, but some selective ones (other than the call caching enabling option that is currently available on Terra) that are safe and useful to expose to users would be just as good.
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