Various Part Transactions add costs to WIP. Like STK-MTL or PUR-MTL. Pretty much most that have a type ending with “-MTL”.
User initiated transactions that remove costs from WIP include: MFG-CUS (customer shipment), and MFG-STK (receipt from Job to Inventory). Pretty much most that start with “MFG-”.
The cost method you use can affect this. Say you use STD costing, and the STD cost of the part being made for stock, is $1,000. If $1,050 was issued to the job, then the part was received to inventory, Inventory would increase by $1,000, and WIP would decrease by $1,000. That would leave $50 (related to the job), still in WIP. When the Job is closed, the system will make a MFG-VAR transaction to remove that last $50 from WIP.