It's hard to determine with certainty because we don't have access to real-time information on the cash needs of individual departments and agencies, and certainly not at a disaggregated enough level to determine which programs would be at risk.
Generally speaking, departments and agencies lapse money. They're allowed to lapse up to 5% of their operating spending and carry it forward. In most cases, it would mean that the lapse they could carry forward to the next year would be lower. I don't think many, if any, departments and agencies would have to stop operations before the end of the fiscal year, but again, specific ministers would be in a better position to determine whether or not they would run out of cash.