https://github.com/chelauk/nf-core-deepsnv

processing tumour normal pairs with deepsnv

https://github.com/chelauk/nf-core-deepsnv

Repository

processing tumour normal pairs with deepsnv

https://github.com/chelauk/nf-core-deepsnv/blob/master/

# ![nf-core/deepsnv](docs/images/nf-core-deepsnv_logo.png)

**processing bams through deepsnv**.

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
[![Docker](https://img.shields.io/docker/automated/nfcore/deepsnv.svg)](https://hub.docker.com/r/nfcore/deepsnv)
[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23deepsnv-4A154B?logo=slack)](https://nfcore.slack.com/channels/deepsnv)

## Introduction

The pipeline is built using [Nextflow](https://www.nextflow.io), 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`](https://nf-co.re/usage/installation)

2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Podman`](https://podman.io/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_

3. Download the pipeline and test it on a minimal dataset with a single command:

    ```bash
    nextflow run nf-core/deepsnv -profile test,
    ```

    > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` 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!

    

    ```bash
    nextflow run nf-core/deepsnv -profile  --input '*_R{1,2}.fastq.gz' --genome GRCh37
    ```

See [usage docs](https://nf-co.re/deepsnv/usage) for all of the available options when running the pipeline.

## Documentation

The nf-core/deepsnv pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/deepsnv/usage) and [output](https://nf-co.re/deepsnv/output).



## Credits

nf-core/deepsnv was originally written by chela james.

## Contributions and Support

If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).

For further information or help, don't hesitate to get in touch on the [Slack `#deepsnv` channel](https://nfcore.slack.com/channels/deepsnv) (you can join with [this invite](https://nf-co.re/join/slack)).

## Citation




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](https://dx.doi.org/10.1038/s41587-020-0439-x).
> ReadCube: [Full Access Link](https://rdcu.be/b1GjZ)

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