Whisk together flour, wheat germ, salt and baking soda. Set aside.
With an electric mixer, beat butter and both sugars until creamy. Beat in vanilla. Add the eggs one by one, beating for 30 seconds after each egg.
Stir flour mixture into butter mixture, followed by oats, chocolate chips and pecans. Chill dough for 1 hour if needed (if you weighed the flour you probably won't have to).
Preheat oven to 350 degrees F. Drop dough by generously rounded teaspoonfuls onto ungreased cookie sheets.
Sprinkle tops with a little sea salt, then bake for 8 to 12 minutes. Let cool on cookie sheet for 3 minutes. Remove and cool on wire rack.
Makes about 60 cookies