I lived out of the home. My spouse, who was unemployed, lived in the home with our two children. Not sure how to file.

By "separated", do you mean there was a legal action filed for spousal separation (often a prelude to divorce), or were you simply not living with your spouse?

In either case, if you were not legally divorced last year, I believe you can file a joint US federal income tax return (assuming that's what you mean). Compute your taxes both ways (married, filing jointly, or married, filing separately) to determine which would be best for you, but if I had to guess, I'd say a joint return would be best.