Snakemake Tutorial

Table of Contents

1. Introduction
2. Installation
3. Basic Concepts
4. Run via Gitpod
5. Tutorials

Introduction

Snakemake is a workflow management system that enables the creation of reproducible and scalable data analyses. It is particularly popular in the bioinformatics community but is applicable to any field where workflows are essential.

Installation

To install Snakemake, you can use conda or pip.

# Using conda
conda install -c bioconda snakemake

# Using pip
pip install snakemake

Basic Concepts

• Rule: Defines a step in the workflow.
• Workflow: A combination of rules specifying the entire data analysis pipeline.
• Snakefile: The file where the workflow is defined.

Run via Gitpod

The easiest way to try Snakemake is to use Gitpod, via your browser through this predefined snakemake-tutorial GitPod, which includes all required software, for free and in the cloud.

Tutorials

• Basic Snakemake
• Advanced Snakemake
• Additional Features