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Heat oven to180C/160Cfan/gas 4. Lightly oil 12 holes of a muffin tin.
Pull apart any squash spirals that are still stuck together and cut any long spirals of squash in half. Heat the oil in a frying pan over a medium heat then add the spiralized squash and red onion. Cook, stirring occasionally for 3 mins until the vegetables have softened slightly. Stir in the red chilli, fry for a further min then remove from the heat and allow to cool slightly.
Beat the eggs in a large jug or bowl and season with salt and a generous grind of black pepper. Stir in the butternut squash mixture along with the thyme leaves and goat’s cheese.
Divide the mixture between each muffin tin, making sure each hole gets an equal amount of filling, then bake in the oven for 15–18 mins or until just set. Gently lift the fritattas out of the tin with a palette or cutlery knife.
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