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We do this in the wf-editor and in the backend, so this works for subworkflows. This should make quite some tools more usable in a workflow scenario. Should fix - https://github.com/galaxyproject/galaxy/issues/6514 - https://github.com/galaxyproject/galaxy/issues/6012 - https://github.com/galaxyproject/galaxy/issues/6569 - https://github.com/galaxyproject/galaxy/issues/1889 and perhaps more issues related to this.