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.
This workflow development is currently based on:
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
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
singularityand 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
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
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 :)
Listed in alphabetical order
If you would like to contribute to this pipeline, please see the contributing guidelines.
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.