Since she lived in the US all 12 months of the year, she would be considered a resident alien for the time prior to becoming a lawful permanent resident. A resident alien files a 1040 form, not a 1040NR. Therefore, since you were both residents (living in the US) the entire year you can simply file a regular tax return as Married Filing Jointly or Married Filing Separately. Generally, Married Filing Jointly provides a better result tax wise.
[Edited 1/22/18 8:42PM]
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