The reproducibility nightmare
Regarding your bullet points, these are all valid points, but they apply to all computing environments. Even a cloud computer is still just a virtual computer that presents itself to you as a simple Bash shell in 99% of cases. Even with the best intentions to implement a standardized workflow, people will likely start experimenting using trial and error on the way, using different tools, reference genomes, and ad hoc format conversion with the awk command they found on Biostars. QC will be unsatisfying for some samples, so they are removed, possibly running everything from scratch. Possibly the result of some tool was not consistent, so we replaced it with another one or upgraded the version in conda. Except of course that one single tool that was not available in Conda so we installed it from source. But later on, we also installed the tool with conda (because it turned out it was available anyway) without specifying the version.
Now we have the output of both versions lying around, but which was which, and is the version of the tool that is installed now identical to what we used earlier?
Of course, we do not call our commands specifying the full path to the executable, because normally we will assume we have only a single program of that name in our PATH ever. So it turns out we are not exactly sure which program and version we used for this analysis.
Hopefully, the tool has written its provenance information into the log or the output file...
Now, the only tool Bash (your "work-flow" interface) provides to alleviate this is .bash_history but it is going to be a mess. Also, we have a habit of running everything on wildcards (do_stuff.sh *.sam) but you had to delete some of the files in the meantime due to space problems. So in the end you have no clue what you effectively ran your stuff on either.
There are also these nasty tools that allow you or even require you to specify vital parameters interactively. You desperately wanted to avoid this but fatigue set in and you didn't feel like sorting out how to specify these minor parameters on the command line, if it was possible even. Of course, there is no record of your interactions in the bash_history, and therefore you are now completely clueless about which parameters you ran your analysis with.
Finally, you notice that as a result of or despite your efforts, you do not know which program or what version of it you ran on what data using a set of parameters you can only vaguely remember. So you wish you had written the whole analysis in snake-make from the get-go, but there was so much experimentation and tuning involved (it is scientific data after all).
So, if you want to solve something with AI here, you could implement a tool that "understands" what you are doing, optimally also understands the tools and their output, hooks into bash and turns your history into a correct snake-make workflow. Also, when you want to do funny things like installing "the latest" version of a tool without specifying a version it will warn you with a pop-up window to prevent such stupidity.
Remember me if you get rich and famous with the idea.