nfcore/rnafusion repository overview

Nextflow rnafusion analysis pipeline, part of the nf-core community..

⁠Introduction

nf-core/rnafusion is a bioinformatics best-practise analysis pipeline for identifying gene fusions from RNA-seq experiments.

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 any of Docker⁠, Singularity⁠ or Podman⁠ 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 nf-core/rnafusion -profile test,<docker/singularity/podman/conda/institute>
   

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   Please check nf-core/configs⁠ to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

4. Start running your own analysis!

   nextflow run nf-core/rnafusion -profile <docker/singularity/podman/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
   

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

⁠Pipeline Summary

By default, the pipeline currently performs the following:

• Sequencing quality control (FastQC)
• Overall pipeline run summaries (MultiQC)

⁠Documentation

The nf-core/rnafusion pipeline comes with documentation about the pipeline: usage⁠ and output⁠.

⁠Credits

nf-core/rnafusion was originally written by Martin Proks.

We thank the following people for their extensive assistance in the development of this pipeline:

⁠Contributions and 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 the Slack #rnafusion channel⁠ (you can join with this invite⁠).

⁠Citations

You can cite the nf-core publication as follows:

In addition, references of tools and data used in this pipeline are as follows: