You would file one federal tax return and a part-year resident return for your spouse for the time she was in Minnesota. For the state return, you can file it married-joint or married-separate, whichever way turns out best. If you file it married-separate, you will have to prepare a separate federal return entering her tax information only to populate the married-separate Minnesota return. For that one, you don't submit the federal return, just the Minnesota one.
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