Sometimes it's prudent to not have an athlete perform a barbell squat for their main movement.
This could be because of structural changes in the hip (FAI, as an example), a shoulder injury, low back pain, or perhaps the because of the time of year (in-season, early off-season, etc.), or any number of other reasons why a strength coach or trainer may decide not to put it in their program for that wave.
The great news is, despite the fact that the squat is often heralded as the "king of all exercises," there other ways of to induce a similar training effect if the time calls for it.
While there are many possible alternatives, one great substitute is the barbell stepback lunge with front squat grip:
You still receive all the benefits of axial loading, along with a healthy dose of a strength stimulus for the lower body and core. Not to mention, there's something about this exercise that really gasses you, even if you keep the reps toward the lower end of the spectrum.
Give it a shot. I think you'll like it, even though your athletes may curse you for its inclusion in their program.