Unfortunately, you cannot use the Free Edition to file a return reporting HSA contributions.
The IRS requires that you file form 8889 if there were any contributions to your HSA (from anyone, including your employer) or any distributions from your HSA in 2018.
Form 8889 is not part of the Free Edition, so you will have to upgrade to Deluxe in order to file your return.
You actually got a deduction advantage with the contribution amount because when the code W was placed in box 12 on your W-2, the code W amount was also removed from your Wages in boxes 1, 3, and 5 at the same time. Although the advantage is not obvious, this contribution reduced your taxable income by the code W amount.
The IRS got a copy of your W-2 with the code W. If you file a return without form 8889, then the IRS will write you a letter asking where it is - at that point, you'll have to add the 8889 anyway.