Currently, if all intermediate files are removed, snakemake would do nothing. But in most cases, we want to regenerate all the results. Of course, we can delete all downstream files and everything is working well. However, it is a little bit anti-intuition. What do you think?
Well, if upstream files are updated, we may want to update all the results even some intermediate files are missing.
Yes that is correct. In such a case you want an update. Seems like a bug due to some rewrites. I am looking into it right now.
Great work Jianxing, that was a very tiny typo with rather big consequences. I fixed it in commit f2cd74f.