Hi, I was wondering how you prevent MAG from runnning again from scratch when you change a single command that only affects very late stages of the pipeline? e.g. --refine_bins_dastool

I'm not sure is this is the official way, but I always start with the -resume option (with one dash), even when starting from scratch). I was in the exact same position and managed to rerun with --refine_bins_dastool although I still need to evaluate if the Taxonomy output is rerun

Yes,

-resume

is the official option. Personally I have

resume = true

in

~/.nextflow/config

to prevent forgetting to add the option and break the cache. But keep in mind that even with resume the pipeline could not start exactly where is was before, because some processes could run again if trey retried and that changed the command (i.e. dynamic cpus or memory).