Snk: A Snakemake CLI and Workflow Management System

Abstract

Snk (pronounced “snek”) is a workflow management tool designed to simplify the use of Snakemake workflows by dynamically generating command-line interfaces (CLIs). Snk allows complex Snakemake workflows to be used as modular components in larger systems that can be executed and managed from the command line with minimal overhead. This enables researchers and developers to integrate and manage sophisticated workflows seamlessly. Snk significantly improves the interoperability and accessibility of Snakemake workflows, making it easier to use and share computational pipelines in various research fields.