RNA-SEQ

A workflow for RNA-seq analysis in Snakemake.

Table of Contents

• Introduction
• Requirements
• Usage
• Contributing
• Thanks
• License

Introduction

This workflow is a bioinformatics analysis pipeline for RNA sequencing data. The workflow is built using Snakemake - a scalabale bioinformatics workflow engine

Requirements

This workflow requires the following software to run:

• [Snakemake][snakemake]
• [Conda][code]

Usage

Clone workflow into working directory:

git clone https://github.com/jma1991/rnaseq.git

Execute workflow and deploy software dependencies via conda:

snakemake --use-conda

Configuration

Configure the workflow by editing the files in the config directory:

• config.yaml is a YAML file containing the workflow metadata.

• samples.csv is a CSV file containing the sample metadata.

• units.csv is a CSV file contains the unit metadata.

Contributing

To contribute to the workflow, clone this repository locally and commit your code on a separate branch. Please generate unit tests for your code, and run the linter before opening a pull-request:

snakemake --generate-unit-tests # generate unit tests
snakemake --lint # run the linter

You can find more detail in our Contributing Guide. Participation in this open source project is subject to a Code of Conduct.

Thanks

I would like to thank Johannes Köster for developing the Snakemake workflow engine and Istvan Albert for writing the biostar handbook.

License

This workflow is licensed under the MIT license.
Copyright © 2020, James Ashmore