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Harpy relies on Snakemake under the hood to handle file and job dependencies. Most of these details have been abstracted away from the end-user, but most Harpy modules have an optional flag --snakemake that you can use to augment -the Snakemake workflow if necessary. Whenever you use this flag, your argument -must be enclosed in quotation marks, for example:

+the Snakemake workflow if necessary. The full list of Snakemake command line +options can be found here. +Whenever you use this flag, your argument must be enclosed in quotation marks, for example:

harpy qc --snakemake "--dry-run" rawseq
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