# SD8.1 Programming Snakemake Workflows

## Requirements

* [[skill-tree:use:1:3:b]]
* Python Programming

## Learning objectives

* Develop Snakemake workflows by utilising rules, input/output files, and directives such as shell, script, run, "wrappers", and resource definitions.
* Integrate custom Python scripts into Snakemake workflows for dynamic data manipulation and resource parameterization.
* Handle automatic software deployment using Conda, or software provisioning with Apptainer/Singularity or module files.
* Modularize existing Snakemake workflows into semantic units to improve maintainability and scalability.