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nfcore/covid19

By nfcore

•Updated over 6 years ago

A docker container for nf-core/covid19.

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nfcore/covid19 repository overview

nf-core/covid19

GitHub Actions CI Status GitHub Actions Linting Status Nextflow

install with bioconda Docker

⁠Introduction

The pipeline is built using Nextflow⁠, 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.

⁠Pipeline summary

This workflow development is currently based on:

Initial analysis of COVID-19 data using Galaxy, BioConda and public research infrastructure (XSEDE, de.NBI-cloud, ARDC cloud)⁠

No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics

usegalaxy.org, usegalaxy.eu, usegalaxy.org.au, usegalaxy.be and hyphy.org development teams, Anton Nekrutenko, Sergei L Kosakovsky Pond.

bioRxiv 2020.02.21.959973; doi: 10.1101/2020.02.21.959973⁠

⁠Quick Start

i. Install nextflow⁠

ii. Install either Docker⁠ or Singularity⁠ for full pipeline reproducibility (please only use Conda⁠ as a last resort; see docs⁠)

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

nextflow run nf-core/covid19 -profile test,<docker/singularity/conda/institute>

Please check nf-core/configs⁠ to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

iv. Start running your own analysis!

nextflow run nf-core/covid19 -profile <docker/singularity/conda/institute> --input samplesheet.csv --genome hg38

See usage docs⁠ for all of the available options when running the pipeline.

⁠Documentation

The nf-core/covid19 pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation⁠
  2. Pipeline configuration
  3. Running the pipeline⁠
  4. Output and how to interpret the results⁠
  5. Troubleshooting⁠

⁠Credits

The implementation of nf-core/covid19 is an international collaboration between numerous contributors and developers. We appreciated the need to have a portable, reproducible and scalable pipeline for the analysis of COVID-19 sequencing samples and so we assembled to do our bit! Please come and join us :)

⁠Contributor list
NameAffiliation
Alexander Peltzer⁠Boehringer Ingelheim, Germany⁠
Edgar Garriga Nogales⁠Centre for Genomic Regulation, Spain⁠
Edmund Miller⁠University of Texas at Dallas, USA⁠
Harshil Patel⁠The Francis Crick Institute, UK⁠
Jordan Wilheim⁠University of California, USA⁠
Jose Espinosa-Carrasco⁠Centre for Genomic Regulation, Spain⁠
Lukas Heumos⁠Quantitative Biology Center, Germany⁠
Maxime Garcia⁠SciLifeLab, Sweden⁠
Michael L Heuer⁠University of California, Berkeley, USA⁠
Phil Ewels⁠SciLifeLab, Sweden⁠
Santiago Revale⁠The Wellcome Centre for Human Genetics, UK⁠
Thanh Le Viet⁠Quadram Institute, UK⁠
Tobias Schraink⁠New York University, USA⁠

Listed in alphabetical order

⁠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 Slack⁠ (you can join with this invite⁠).

⁠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. ReadCube: Full Access Link⁠

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over 6 years ago

docker pull nfcore/covid19