Heat 1 tablespoon olive oil over medium heat in a large saute pan. Add chopped butternut squash and saute until lightly browned, about 6-7 minutes. The butternut squash should be getting tender but won't be completely cooked.
Add chopped red onion and saute until tender, about 4 minutes. Add sausage, breaking it up into smaller chunks. Saute until sausage is browned, about 3 minutes.
Add garlic, swiss chard, and red chili flakes. Continue to cook until chard is wilted, another 3 minutes. Season mixture with salt and pepper and keep warm.
While vegetables and sausage are cooking, bring a pot of salted water to a boil. Cook rigatoni until al dente, about 8 minutes. Drain pasta, reserving ¼ cup of the pasta water.
Immediately add cooked rigatoni to sausage mixture along with ¼ cup reserved pasta water, creme fraiche, and grated parmesan. Stir to coat pasta in the sauce and continue to cook for 1-2 minutes. Season with salt and pepper. Sprinkle extra parmesan on top and serve immediately.
Notes
To make this pasta vegetarian, use spicy vegetarian sausage or soyrizo.