Works Contract of Government Tenders under existing Composition scheme Migrating to GST

Works Contract of Government Tenders under existing Composition scheme Migrating to GST present VAT. VAT is added reimbursed and paid directly by the department on running bills as it was not added in the Estimate while tender itself. Service tax is exempted and not applicable as per present act, so no add or deduct of ST and we were not getting input credit for purchases. Now after GST how will the GST rate be passed to the contractor from the department. And regarding Stock Input, Work in Progress, New Items not in estimates, Price adjustment Clause reimbursements of preceeding years shall be paid on final bills only but work was executed much before final Billing. How will we be credited please advise.