Cluster Flow: A user-friendly bioinformatics workflow tool [version 1; referees: 3 approved]

Abstract

ns4:p>Pipeline tools are becoming increasingly important within the field of bioinformatics. Using a pipeline manager to manage and run workflows comprised of multiple tools reduces workload and makes analysis results more reproducible. Existing tools require significant work to install and get running, typically needing pipeline scripts to be written from scratch before running any analysis. We present Cluster Flow, a simple and flexible bioinformatics pipeline tool designed to be quick and easy to install. Cluster Flow comes with 40 modules for common NGS processing steps, ready to work out of the box. Pipelines are assembled using these modules with a simple syntax that can be easily modified as required. Core helper functions automate many common NGS procedures, making running pipelines simple. Cluster Flow is available with an GNU GPLv3 license on GitHub. Documentation, examples and an online demo are available at <ns4:ext-link xmlns:ns3="http://www.w3.org/1999/xlink" ext-link-type="uri" ns3:href="http://clusterflow.io">http://clusterflow.io</ns4:ext-link>.</ns4

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The different versions of the original document can be found in:

• http://dx.doi.org/10.12688/f1000research.10335.1 under the license https://creativecommons.org/licenses/by

• http://europepmc.org/articles/PMC5310375 under the license http://creativecommons.org/licenses/by/4.0

• https://dx.doi.org/10.12688/f1000research.10335.1

• https://f1000research.com/articles/5-2824/v1/pdf

• https://f1000research.com/articles/5-2824/v2/pdf under the license cc-by

• https://f1000research.com/articles/5-2824/v1,

https://doaj.org/toc/2046-1402 under the license cc-by

• https://f1000research.com/articles/5-2824/v1/xml,

https://f1000research.com/articles/5-2824/v1/pdf,

https://f1000research.com/articles/5-2824/v1/iparadigms,

http://dx.doi.org/10.12688/f1000research.10335.1

• https://f1000research.com/articles/5-2824/v2,

https://doaj.org/toc/2046-1402 under the license http://creativecommons.org/licenses/by/4.0/

• https://f1000research.com/articles/5-2824/v2/xml,

https://f1000research.com/articles/5-2824/v2/pdf,

https://f1000research.com/articles/5-2824/v2/iparadigms,

http://dx.doi.org/10.12688/f1000research.10335.2

• https://www.ncbi.nlm.nih.gov/pubmed/28299179,

http://europepmc.org/abstract/MED/28299179,

http://www.diva-portal.org/smash/record.jsf?pid=diva2:1103947,

https://academic.microsoft.com/#/detail/2560581264 under the license http://creativecommons.org/licenses/by/4.0/

DOIS: 10.12688/f1000research.10335.1 10.12688/f1000research.10335.2