nf-core/rnadnavar

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Introduction

The *nf-core/rnadnavar* is a bioinformatics best-practice
analysis pipeline for Pipeline for RNA and DNA
integrated analysis for somatic mutation detection.

Initially designed for cancer research, the pipeline
uses different variant calling algorithms and applies a
consensus approach. A final filtering stage, should
provide a set of annotated somatic variants.

The pipeline is built using Nextflow, a workflow tool to run tasks across
multiple compute infrastructures in a very portable
manner. It uses Docker/Singularity containers making
installation trivial and results highly reproducible.
The Nextflow DSL2 implementation of this
pipeline uses one container per process which makes it
much easier to maintain and update software
dependencies. Where possible, these processes have been
submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

Pipeline summary

1. Read QC (FastQC)
2. Present QC for raw reads (MultiQC)
3. Alignment (BWA/STAR)
4. GATK pre-processing
5. Variant calling
6. Normalise calls
7. Annotation
8. Consensus
9. Filtering
10. Realignment [OPT]
11. RNA filtering

Usage

*Note*
If you are new to Nextflow and nf-core, please refer to this page on how
to set-up Nextflow. Make sure to test your setup
with -profile test before running the workflow on actual data.

Now, you can run the pipeline using:

nextflow run nf-core/rnadnavar \  
   -profile <docker/singularity/.../institute> \  
   --input samplesheet.csv \  
   --outdir <OUTDIR>  

*Warning:*
Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those
provided by the -c Nextflow option can be used to provide any configuration *except for parameters*;
see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.
For more details about the output files and reports, please refer to the
output documentation.

Credits

The nf-core/rnadnavar was originally written by Raquel
Manzano Garcia at Cancer Research UK Cambridge Institute
with the initial and continuous support of Maxime U
Garcia. The workflow is based on
RNA-MuTect which was
originally published by Yizhak, *et al* 2019 (Science)

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

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 #rnadnavar channel (you can join with this invite).

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

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.