Since I am new to this, I'm not sure what I like more. I have also been self-teaching before this course but have not gotten deep into a particular language's fundamentals. I want to decide on a language and stick to it before I move to a new one after the first language is learned, but it is difficult deciding which language to start with. I want to develop medical software and medical mobile apps.
Since you're already taking a CS course which involves Java, I would recommend you to keep learning it. Java's statically typed & OO nature forces you to learn a lot of important yet common programming fundamentles. C++, C# and Java type languages also force you write code more carefully (you have to think about the data types on your own and even allocate/de-allocate memories [C++ pointers]). That's why colleges prefer it as go to language for teaching CS concepts.
On the other hand, JS, Python and other such languages are dynamic in nature and hence, easy to learn. But you can't learn certain concepts (polymorphism, abstract classes, diamond problem etc) using these languages. So it makes sense to stick with Java in your case.
Sticking to a language before moving on is a common goal. However, in reality you are going to transition as you find languages that better suit you or your organization's requirements. Start with Java, not because it is optimal for your end goals, but because it will teach you what you like and dislike about programming and because your instructor is more familiar with it. That will give you a valuable perspective and allow you to make a more informed decision later.
There are many ways to solve problems in different languages, but the "best" language pragmatically is the one that you feel most comfortable using. In that respect, programming is like woodworking- you want to let the tool do the work. If there is another language that is "better" objectively but more difficult or confusing to you, you will counteract the anticipated benefits by having to struggle to write code.