That's a matter of your process. However, a simple, and commonly used option with JIRA is to simply close it and put the "duplicate" resolution on it while doing so. More complex variations might include transitions for "resolve as a duplicate" that would set the resolution for you and probably prompt for a link to the original.
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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