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!

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Pipeline summary

<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
  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
<p align="center"> <img title="Sarek Workflow" src="docs/images/rnadnavar_schemav2.png"> </p>


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.

<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets. Explain what rows and columns represent. For instance (please edit as appropriate): First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: ```csv sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz ``` Each row represents a fastq file (single-end) or a pair of fastq files (paired end). -->

Now, you can run the pipeline using:

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

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.


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:

<!-- TODO nf-core: If applicable, make list of people who have also contributed -->

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).


<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. --> <!-- If you use nf-core/rnadnavar for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX]( --> <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->

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