Thaw the spinach and squeeze to remove any excess water in paper towels.
In a medium bowl, combine the cottage cheese, Parmesan cheese, garlic, pepper, red pepper flakes, and drained spinach; set aside.
Carefully boil the cannelloni shells in two batches for approximately 6 to 8 minutes, or until cooked but still slightly firm. Do not overcook.
Fill a piping bag (without a tip) or a large zipper bag with a hole cut on one end with the cottage cheese mixture and pipe the filling into the cooked pasta shells.
Spread 1/3 of the tomato sauce on the bottom of a 13x9-inch baking dish. Line the dish with the cannelloni and pour the remaining sauce evenly over the top.
Cover the dish with aluminum foil and bake for 35 minutes at 350 degrees.