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I have implemented this in the main branch, please try it out before I make a release out of it.
You can add clearOnJobDone: true to the sourceFileSystem block in the config file. It deletes any files that are actual inputs to the workflow from that directory. So I wouldn't use it if you reuse files in the sourceFileSystem.
It does not (and cannot) delete any directories you may have created in the sourceFileSystem.
I would like to be able to delete the input files that are in the sourceFileSystem, after a job has completed or failed.
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