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In the "Raise Direct Invoice" page itself, GRN will be done automatically by the system base on 3 types of quantities, 1- Invoice QTY, 2- Accepted QTY and 3- Rejected QTY.  which has to be filled. For GRN system will consider accepted QTY only and accordingly inventory register will be updated based on accepted QTY. 

Yes, in the Inventory register goods will be counted as received and accordingly closing stock will be increased once the direct Invoice will be approved.