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Snakemake Command Cheat Sheet

Snakemake Description
snakemake -h help page with all Snakemake flags
snakemake -n <rule name> a dry run of the rule commands without actually running them, good for testing
snakemake -p <rule name> print shell commands to terminal as you run through the specified rule commands
snakemake --delete-all-output <rule name> delete all the outputs up to a certain rule if specified, otherwise only output of first rule by default

Last update: April 2, 2021