In a large measuring cup, heat water to approximately 110º and sprinkle yeast over water. Stir to combine, gently, and let sit for about 10 minutes until frothy.
Meanwhile, in a food processor fitted with a dough blade (I used a mixer with a dough blade), combine all dry ingredients and pulse to combine.
Add egg and yeast mixture and pulse in short bursts until the dough comes together. Do not over mix, you just want the dough to come together.
Turn out onto a lightly floured surface and knead a few times with your hands. If dough feels sticky, add a little more flour. Form the dough into a ball and cut in half.
Roll out 1/2 of the dough into a large rectangle, approximately 12"x17", sprinkle about 3/4 cup of the colby jack cheese down the center 1/3 of the dough. Fold one edge over the cheese and sprinkle with another 3/4 cup of cheese. Fold over the remaining 1/3 dough and pinch edges to seal cheese inside.
Roll out the dough again into an 11"x15". Cut the dough into six strips approximately 1 1/2 inches wide. Roll each strip into a tube and form into a pretzel shape by looping and crossing the ends over each other, then tuck back onto the loop and pinch to seal. Repeat with remaining dough.
Preheat oven to 425º. In a small bowl, combine remaining egg and milk. Whisk to combine and set aside.
In another small bowl, combine poppy seeds, garlic, onion, and salt. Brush the pretzels liberally with the egg wash, then sprinkle with spice mixture.
Bake 18-20 minutes until light golden brown. Transfer pretzels to a wire rack to cool.