hyperfine with snakemake

[TolgaDuz]

Hi,

i want to benchmark a snakemake-pipeline of mine. In snakemake one specifies a higher rule, called rule all, which must be achieved by smaler rules. after finishing rule all, a re-execution cannot happen if the outputfiles are already generated. so therefore i always have to delete the output files to run snakemake again, in order to benchmark the pipeline. How can i subtract the execution time for the removal of the outputfiles from my final results?

thanks, Tolga

[sharkdp]

This is exactly what --prepare and --cleanup are for. Please see the man page / README for more information.