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This pipeline has moved!

This pipeline has been moved to the new nf-core project. You can now find it here:

https://github.com/nf-core/sarek

If you have any problems with the pipeline, please create an issue at the above repository instead.

To find out more about nf-core, visit http://nf-co.re/

This repository will be archived to maintain the released versions for future reruns, in the spirit of full reproducibility.

If you have any questions, please get in touch: support@ngisweden.se

// Maxime Garcia, 2020-01-27

An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing

Nextflow version Travis build status Join the chat on https://gitter.im/SciLifeLab/Sarek

MIT License Sarek version DOI

Install with bioconda Docker Container available

Introduction

<img align="right" title="CAW" src="https://raw.githubusercontent.com/SciLifeLab/Sarek/master/docs/images/CAW_logo.png">

Previously known as the Cancer Analysis Workflow (CAW), Sarek is a workflow designed to run analyses on WGS data from regular samples or tumour / normal pairs, including relapse samples if required.

It's built using Nextflow, a domain specific language for workflow building. Software dependencies are handled using Docker or Singularity - container technologies that provide excellent reproducibility and ease of use. Singularity has been designed specifically for high-performance computing environments. This means that although Sarek has been primarily designed for use with the Swedish UPPMAX HPC systems, it should be able to run on any system that supports these two tools.

Sarek was developed at the National Genomics Infastructure and National Bioinformatics Infastructure Sweden which are both platforms at SciLifeLab. It is listed on the Elixir - Tools and Data Services Registry.

Workflow steps

Sarek is built with several workflow scripts. A wrapper script contained within the repository makes it easy to run the different workflow scripts as a single job. To test your installation, follow the tests documentation.

Raw FastQ files or aligned BAM files (with or without realignment & recalibration) can be used as inputs. You can choose which variant callers to use, plus the pipeline is capable of accommodating additional variant calling software or CNV callers if required.

The worflow steps and tools used are as follows:

  1. Preprocessing - main.nf (based on GATK best practices)
  2. Germline variant calling - germlineVC.nf
  3. Somatic variant calling - somaticVC.nf (optional)
  4. Annotation - annotate.nf (optional)
  5. Reporting - runMultiQC.nf

Documentation

The Sarek pipeline comes with documentation in the docs/ directory:

  1. Installation documentation
  2. Installation documentation specific for UPPMAX rackham
  3. Installation documentation specific for UPPMAX bianca
  4. Tests documentation
  5. Reference files documentation
  6. Configuration and profiles documentation
  7. Intervals documentation
  8. Running the pipeline
  9. Running the pipeline using Conda
  10. Command line parameters
  11. Examples
  12. Input files documentation
  13. Processes documentation
  14. Documentation about containers
  15. Complementary information about ASCAT
  16. Complementary information about annotations
  17. Output documentation structure

Contributions & Support

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

For further information or help, don't hesitate to get in touch on Gitter or contact us: maxime.garcia@scilifelab.se, szilveszter.juhos@scilifelab.se

CHANGELOG

Credits

Main authors:

Helpful contributors:

SciLifeLab NGI NBIS