It would be nice to have an option where the automate will skip processing materials if the materials has X number of items left in a chest

Hi! You can tell Automate not to remove the last item in a stack, which also lets you set a minimum (e.g. two stacks of coal = minimum two coal in the chest).

I'll close this ticket since I don't track questions/suggestions on GitHub, but feel free to comment on the Automate mod page if you have any other comments or questions!