Is there a way to set a late submission penalty for quizzes separately than assignments? For online quizzes, I allow students to makeup missed quizzes, but they're subject to a points deduction. I can set a due date, and then make the available until date after the quiz to allow students to still take the quiz, but I'd like for them to be subject to a percentage or points deduction automatically, so I don't have to do a manual override.
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You can't select a different policy for late submissions for quizzes and assignments. The policy will be set for the whole gradebook.
If you don't want the students to be penalized for late assignments, you would need to manually remove the late mark from their submission so they don't get penalized. If you just don't allow late submissions for assignments, you can set the until date the same as the due date, and the assignment will close on that date and they will be marked as "missing".
Here is a guide on setting up late policy
You are welcome to submit an idea to the community for how you would like this to work instead.