Why can't they just take a class on shell scripting? The whole point of computer science is to automate things, because that's what gives you leverage. If you don't care about understanding computer science, at least skip to the point and enjoy the fruits. We've been using the UNIX shell for 50 years. It's not going anywhere.
I'm someone that uses shell scripts in my day to day work (I don't work in biology any more, but did for a while).
I'm saying that for the average scientist using these tools, a shell script is not an easier or more useful tool than Python plus libraries. Can you honestly say that shell scripts are more intuitive and easy to understand than Jupyter notebooks? Are they going to be more easy to transfer to other stakeholders?
This is one of those solutions that seems better in theory, but likely isn't in practice.
I majored in biology. A shell script would be a much more cumbersome tool for making a scatterplot, running a linear regression on a csv, etc.
The things that people are using Python for are significantly easier with Python. There are libraries designed to make these tasks super simple, and with the right IDE you wouldn't ever have to touch the shell.