Genomics England's workflow for variant quality control and annotation.

Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Quick Start

1. Install nextflow

2. Install either Docker or Singularity for full pipeline reproducibility (please only use Conda as a last resort; see docs)

3. Download the pipeline and test it on a minimal dataset with a single command:

   nextflow run lifebit-ai/siteqc -profile test,<docker/singularity/conda/institute>

4. Start running your own analysis!

   nextflow run nf-core/siteqc --input s3://lifebit-featured-datasets/projects/gel/siteqc/input.csv

See usage docs for all of the available options when running the pipeline.

Documentation

The lifebit-ai/siteqc pipeline comes with documentation about the pipeline which you can find in the docs/ directory.

Credits

The siteqc was originally written by Daniel Rhodes and the Genomics England Bioinformatics team.

The Nextflow implementation of the pipeline was developed by Christina Chatzipantsiou for use by Genomics England and collaborators.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citation

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x. ReadCube: Full Access Link