I have that $Y$ is an $\mathcal{F}$-measurable r.v. with $E{|Y|}<\infty$. I define $$X_{n}=E[Y\mid \mathcal{F_{n}}]$$ I want to compute $E[|X_n|]$. Is it correct that, by applying tower rule, we get the following?
$$E[|X_n|]=E|E[Y\mid \mathcal{F}_n]|=|E[Y]|$$
Or the correct result is the following
$$E[|X_n|]=E|E[Y\mid \mathcal{F}_n]|=E[Y]$$ with $E[Y]$ not in absolute value?
Both are false. You can only say that $E|X_n| \leq E|Y|$.
Tower rule works when you don't have absolute value signs.
Proof of the inequality:
$|Y| -Y \geq 0$ and this implies $E(|Y||\mathcal F_n) \geq E(Y|\mathcal F_n)$. Similarly, $E(|Y||\mathcal F_n) \geq -E(Y|\mathcal F_n)$ and hence $E(|Y||\mathcal F_n) \geq |E(Y|\mathcal F_n)|$. Now take expectation on both sides.