I'm very new to snakemake, and I downloaded a package from github that utilize snakemake, I managed to run it once, but since my data is so large, it took 27 hours to complete the whole thing, but around 99% of it is spent on executing 1 rule, so I wanted to skip that particular rule, when the output file of that rule has already existed. Is snakemake going to skip that rule automatically if the output file of that rule is listed in the rule all section? else, what should I do to skip it?
1 Answers
From the way you describe it, yes, snakemake will skip that long-running rule if its output is already present AND the output is newer than its input. If this second condition is not met, snakemake will run the rule again. This makes sense, right? If the input has been updated then the output is obsolete and needs to be redone. Note that snakemake checks the timestamps not the content of the files.
In practice, you can execute snakemake with the --dry-run option to confirm it is not going to run that rule again. Look also at the --summary option to see why snakemake wants to execute some rules and skip others.
(In doubt, make a copy of the output from the long-running rule, just in case...)
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