There's a slight difference between "going to do" and "will do" something. If you use "will" in this sentence...

Will you be able to make the deadline?

...the question has a different meaning. It's asking the person to make a sort of decision and a promise. If she answers "yes" it means that she's decided that she will be able to On the other hand, when you use "going to", you're making a prediction. So in the example above, the speaker is asking the listener if she thinks she will probably finish on time.