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G-Sarah committed Jan 5, 2023
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[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/chipseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3240506-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3240506)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
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## Quick Start

1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)

2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.

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These scripts were originally written by Chuan Wang ([@chuan-wang](https://github.com/chuan-wang)) and Phil Ewels ([@ewels](https://github.com/ewels)) for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/) at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden. The pipeline was re-implemented by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and converted to Nextflow DSL2 by Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/).

The pipeline workflow diagram was designe by Sarah Guinchard ([@G-Sarah](https://github.com/G-Sarah)).

Many thanks to others who have helped out and contributed along the way too, including (but not limited to): [@apeltzer](https://github.com/apeltzer), [@bc2zb](https://github.com/bc2zb), [@crickbabs](https://github.com/crickbabs), [@drejom](https://github.com/drejom), [@houghtos](https://github.com/houghtos), [@KevinMenden](https://github.com/KevinMenden), [@mashehu](https://github.com/mashehu), [@pditommaso](https://github.com/pditommaso), [@Rotholandus](https://github.com/Rotholandus), [@sofiahaglund](https://github.com/sofiahaglund), [@tiagochst](https://github.com/tiagochst) and [@winni2k](https://github.com/winni2k).

## Contributions and Support
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