If students use the Canvas Student app on a mobile device, they can write on it and then submit it with the annotations. How do I submit a PDF assignment with annotations in the Student app on my iOS device? But unless your students have iPads or Android tablets I don't know how well that is going to work. I wouldn't want to annotate or write on an assignment using my phone.
Sometimes paper just works best. So one alternative I'll mention is to have your students print out the assignment (possibly by you providing a copy in PDF), they write on it or do whatever they need. Then they use a combination of an App named CamScanner to take a picture of the assignment and convert it to PDF, and submit it though Canvas Student to you. I've math and science instructors do this a bit because it's often so important in those areas to see how students worked to come up with a solution. Here is a short video I created showing the process and how a student would submit an assignment this way VidGrid - Using CamScan to create PDF and Submit to Canvas