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Bring 6 quarts water to a boil in a large pot; season with salt.
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Meanwhile, in a 10- to 12-inch skillet, heat olive oil over medium heat until almost smoking.
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Add onion and red pepper flakes;
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Saute until translucent, 8 to 10 minutes.
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Add jalapenos; saute for 1 minute.
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Add zest and juice; bring to a boil, and boil for 1 minute.
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Remove from heat; stir in butter, and season with salt and pepper.
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Set aside.
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Drop pasta into boiling water and cook until tender, 1 to 2 minutes. Drain.
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Toss hot pasta into pan with lemon mixture; return to medium heat.
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Stir together gently.
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Add pecorino; toss quickly. Transfer to a warmed serving platter.
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Serve immediately