Cluster Flow

Cluster Flow is now archived

This project is no longer under active maintenance. You're welcome to use it, but no updates or bug fixes will be posted. We recommend using Nextflow together with nf-core instead.

Many thanks to everyone who used and supported Cluster Flow over the years.

Cluster Flow is designed to be quick and easy to install, with flexible configuration and simple customization.

It's easy enough to set up and use for non-bioinformaticians (given a basic knowledge of the command line), and it's simplicity makes it great for low to medium throughput analyses.

Videos

Simple: Installation walkthroughs and a large module toolset mean you get up and running quickly.
Powerful: Comes packaged with support for 24 different bioinformatics tools (RNA, ChIP, Bisulfite and more).

Flexibile: Pipelines are fast to assemble, making it trivial to change on the fly.
Traceable: Commands, software versions, everything is logged for reproducability.

Read the Docs

Download v0.5

Cluster Flow on GitHub

Cluster Flow Demo

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Cluster Flow Demo

You can try out some basic Cluster Flow commands in this demo terminal.

Step 1
First, let's work out how to use Cluster Flow - try to display the Cluster Flow help. The main Cluster Flow command is cf.
- cf --help
Step 2
Which pipelines, modules and reference genomes do we have available?
- cf --pipelines
- cf --modules
- cf --genomes
Step 3
See if you can find out more information about a pipeline and a module.
- cf --help [pipeline]
- cf --help [module]
Step 4
Add a new reference genome
- cf --add_genome
Step 5
Check the files in your working directory and run a pipeline!
- ls (list files)
- cf [--genome ID] [pipeline] [files]
- eg. cf --genome GRCh37 fastq_bismark *.fastq.gz
Step 6
Monitor the pipeline's progress
- cf --qstat
- qs (usual alias for above)
Step 7
Check the e-mail when the pipeline finishes!
That's it for this demo - feel free to have a play. Better still, grab a copy of Cluster Flow and try it for real!

1. bash

Publication

Cluster Flow has been published in F1000Research - see below for details. If you use Cluster Flow for your research, please consider citing the paper.

Cluster Flow: A user-friendly bioinformatics workflow tool [version 2; referees: 3 approved].
Philip Ewels, Felix Krueger, Max Käller, Simon Andrews
F1000Research 2016, 5:2824
doi: 10.12688/f1000research.10335.2

Cluster Flow is now archived

Videos

Cluster Flow Demo

Cluster Flow Demo

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Publication