Workflow execution: in-place v.s. containerized

[OliverEvans96]

It seems that workflow engines (Toil, CWL, Fireworks) tend to assume that your workflow should be executed with a newly created folder as the working directory. I've figured out how to circumvent this with Fireworks, but the prevalence of this pattern is making me wonder: should we also be insisting that workflows be executed in new folders? It seems that placing as few restrictions on the user as possible is preferable. While there are clear advantages to having a separate working directory for each run of a workflow, sometimes it makes more sense to execute commands within an existing directory.

Other thoughts or links are appreciated.