Mix together flour, rye flour baking soda and salt, and set aside.
In a large mixing bowl, beat butter and brown sugar with an electric mixer until creamy. Add the egg and vanilla and beat until light and fluffy.
Add dry ingredients to butter mixture and mix well to form dough. It should be somewhat dry. Stir in pecans and chocolate chips.
Scoop up level tablespoon of dough and arrange them on a foil lined baking sheet. Don't worry about spacing because this step is just to chill the dough and get the mounds cold.
Chill the dough balls for about an hour or until ready to bake. You should have anywhere from 38 to 42. You can skip this step if you want, but chilling usually improves the shape.
Preheat oven to 375 degrees. Line baking sheets with parchment paper. Arrange balls about 2 inches apart on lined baking sheets and bake 8-10 minutes or until edges are brown and middles appear set. Let cool on baking sheets about 5 minutes, then transfer to wire racks and let cool completely.