Changing rule params in Snakefile doesn't trigger re-run of rule

[rodluger]

I need to look into this -- currently users must touch the actual script that runs the rule for it to be re-run, which is not optimal!

[rodluger]

This seems to be by design on the Snakemake side. Their docs say you can force a re-run of rules with params changes as follows:

snakemake -R `snakemake --list-params-changes`

I suggest we make that the default behavior when calling showyourwork.

[rodluger]

Actually it looks like this behavior changed in Snakemake as of version 7.8: it now does what we want! However, we're pinned at version 6.15.5, and upgrading may or may not break things because of all the hacks we've implemented to enable various showyourwork features. So our choices are -- upgrade the pinned version (and deal with potential breaking changes) or keep it at the current Snakemake version and implement the new functionality of Snakemake on the showyourwork side.