Cook the pasta according to the package directions, drain, reserving 1/2 cup of the pasta cooking water.
Meanwhile, heat the oil in a large skillet or saucepan over medium-high heat. Add the onion and jalapeno and cook for 3 to 5 minutes, until soft. Add the tomato sauce and pesto and bring to a simmer. Reduce the heat to low and simmer for 10 minutes (or until the pasta finishes cooking). Add the pasta with the reserved pasta cooking water and stir to combine. Season to taste with salt and black pepper. Serve with parmesan cheese and crushed red pepper flakes.