Es una pena que no vaya a venir.

English Translation

It is a pity that you’re not going to come.

Shouldn’t it be “vayas”?

It depends on who you’re talking to, whether it’s one or many, the degree of formality, and even which variant of Spanish you speak; it could be any of vaya, vayas, vayan, or vayáis.

I usually deal with this ambiguity by adding a Hint that says “usted”.