Comment by antasvara
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 can't think of a faster easier tool for composing and controlling a bunch of heterogeneous things. Even if you write a Python script that does it, you're still using shell to run it. Notebooks are good for experimenting and explaining, not for automating.