If a task doesn't contain any Atomi content, students have to mark it as done when they have completed the task:

When you add Atomi content however you'll need to choose whether you still want students to mark the task as done or have it automatically marked as done for them once they have completed all the Atomi content:
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By default, the task will be considered done once the Atomi content has been completed when you add Atomi content.

To change that just deselect the 'Task is considered done when Atomi lessons are complete' option. Students can now mark the task as done themselves instead—for when you have included custom instructions or work:

Please note: This option doesn't affect how tasks displays for you or your students, it just removes the onus of having to mark tasks as done for your students if all they have to do is complete the Atomi content in tasks!