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Handle deprecated and deleted modules/subworkflows gracefully #4260

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@SPPearce

Description of feature

If a module/subworkflow is deprecated, we add a failure assertion in the file.
We are now discussing deleting the module/subworkflow entirely after a year or so.
These modules may still bepresent in the modules.json (and pipeline), we need to handle this.
Tools should handle this nicely.

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