https://github.com/dfornika/nf-core-cpo

https://github.com/dfornika/nf-core-cpo

Last synced: 3 months ago
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• Host: GitHub
• URL: https://github.com/dfornika/nf-core-cpo
• Owner: dfornika
• License: mit
• Created: 2018-12-06T00:07:30.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2018-12-06T00:07:45.000Z (over 6 years ago)
• Last Synced: 2025-01-24T23:48:44.668Z (5 months ago)
• Language: Nextflow
• Size: 30.3 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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README

        
# nf-core/cpo

**Genomic Analysis of Carbapenem Resistant Organisms**

[![Build Status](https://travis-ci.org/nf-core/cpo.svg?branch=master)](https://travis-ci.org/nf-core/cpo)

[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg)](https://www.nextflow.io/)

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)

[![Docker](https://img.shields.io/docker/automated/nfcore/cpo.svg)](https://hub.docker.com/r/nfcore/cpo)

![Singularity Container available](

https://img.shields.io/badge/singularity-available-7E4C74.svg)

### 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 / singularity containers making installation trivial and results highly reproducible.

### Documentation

The nf-core/cpo pipeline comes with documentation about the pipeline, found in the `docs/` directory:

1. [Installation](docs/installation.md)

2. Pipeline configuration

    * [Local installation](docs/configuration/local.md)

    * [Adding your own system](docs/configuration/adding_your_own.md)

3. [Running the pipeline](docs/usage.md)

4. [Output and how to interpret the results](docs/output.md)

5. [Troubleshooting](docs/troubleshooting.md)

### Credits

nf-core/cpo was originally written by Dan Fornika.