In a bowl, toss the nectarines with the granulated sugar, juice, thyme and a pinch of salt; let stand for 1 hour.
Preheat the oven to 375°. In another bowl, combine the flour, brown sugar and wheat germ with a pinch of salt. Using your fingers, work in the butter until the mixture is sandy. Press the streusel into small clumps and scatter on a rimmed baking sheet.
Spoon the nectarines, thyme and any juices into 6 individual cast-iron baking dishes. Bake the nectarines for about 20 minutes, until the fruit is softened. Meanwhile, bake the streusel, stirring once, for about 10 minutes, until browned.
Sprinkle the streusel over the fruit, bake for 5 minutes longer and serve.