I help lead the Data Science org at UCSB and generally we take the approach of team driven projects.
For the structure of the project/repo we use the Cookie Cutter Template, although we've created a simplified version of it.
We've picked up on Agile Team Management so we do things like sprints and stand ups while meeting weekly.
We have them create a general outline which can be changed iteratively because often people won't know what the project will look like but keeps them accountable.
We also introduced the concept of milestones, which are simple outlines that help show us and them the progress they've done for each week or meeting time. Here's a simple example, this helps tie the outline together, while having someone be the person in charge of making sure stand ups and blockers are addressed.
Its a learning process but we think we've reaching a timeline we are comfortable with and the biggest hurdle we face right now is the finished product which we're learning more on how to make sure that is satisfactory.