Whisk eggs, milk, salt pepper together. Evenly fill the muffin cups with the broccoli, shallots, cottage cheese and cheddar cheese. The bake at 400 degrees. Bake until the muffins are set and lightly browned around the edges, 12 to 14 minutes. Place the pan on a wire rack and let cool for 2 to 3 minutes. Run a butter knife around each cup to the loosen the muffins before removing them from the pan. Serve warm or cool completely on a wire rack before refrigerating or freezing.