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Bring a large pot of water to a boil. Add the shells and cook according to package directions. Drain into a colander, return shells to the pot and toss with a bit of olive oil to prevent sticking.
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While the shells boil, make the pesto. Place peas, basil, walnuts, olive oil, lemon juice, and garlic into a food processor bowl and pulse until finely chopped and well mixed. Season with salt, pepper, and red pepper flakes to taste. Scoop the mixture into a bowl.
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Next make the ricotta. Place the cashews and milk into the food processor bowl (no need to clean it out first). Blend until smooth. Add the tofu and onion, and pulse until the mixture has a chunky, ricotta-like texture. Add in half of the pea pesto and pulse again just to mix the ingredients. Season with salt and pepper to taste.
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Preheat the oven to 375°.
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Gather a 9 x 13 inch baking pan. Make the sauce by whisking the milk and flour together, right in the baking pan. Add all but about ½ cup of the remaining pea pesto and stir until blended.
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Fill the pasta shells with the ricotta-pea pesto mixture and place them in the baking dish with the sauce.
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Cover the dish and bake 20 minutes. Uncover and bake 5 to 10 minutes more, until the sauce thickens and just begins to bubble.
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Divide shells onto plates and top with reserved pea pesto and additional red pepper flakes, if desired. Serve.