Place the oil in a large sauce pan over medium-high heat. Add the garlic and onion. Saute 3 to 5 minutes until the onions are soft. Add the butternut squash, cinnamon, cumin and season with salt and pepper.
Add the stock and cover. Cook over medium heat until the squash is soft, stirring occasionally, about 25 minutes.
Add the heavy cream and cook for 10 minutes more. Combine sauce and pasta and toss well. Garnish with red pepper flakes and cheese. Serve warm.