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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,,, and 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.


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


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

Name Affiliation
Alexander Peltzer Boehringer Ingelheim, Germany
Edgar Garriga Nogales Centre for Genomic Regulation, Spain
Edmund Miller University of Texas at Dallas, USA
Harshil Patel The Francis Crick Institute, UK
Jordan Wilheim University of California, USA
Jose Espinosa-Carrasco Centre for Genomic Regulation, Spain
Lukas Heumos Quantitative Biology Center, Germany
Maxime Garcia SciLifeLab, Sweden
Michael L Heuer University of California, Berkeley, USA
Phil Ewels SciLifeLab, Sweden
Santiago Revale The Wellcome Centre for Human Genetics, UK
Thanh Le Viet Quadram Institute, UK
Tobias Schraink New 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).


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