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nf-gwas

A nextflow pipeline to perform state-of-the-art genome-wide association studies.

https://github.com/genepi/nf-gwas

Science Score: 65.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
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    Institutional organization owner
    Organization genepi has institutional domain (genepi.i-med.ac.at)
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    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary

Keywords

gwas imputation nextflow regenie singularity slurm
Last synced: 6 months ago · JSON representation ·

Repository

A nextflow pipeline to perform state-of-the-art genome-wide association studies.

Basic Info
Statistics
  • Stars: 65
  • Watchers: 6
  • Forks: 26
  • Open Issues: 10
  • Releases: 54
Topics
gwas imputation nextflow regenie singularity slurm
Created over 4 years ago · Last pushed 11 months ago
Metadata Files
Readme License Citation

README.md

nf-gwas

nf-gwas nf-test

nf-gwas is a Nextflow pipeline to run biobank-scale genome-wide association studies (GWAS) analysis. The pipeline automatically performs numerous pre- and post-processing steps, integrates regression modeling from the REGENIE package and currently supports single-variant, gene-based and interaction testing. All modules are structured in sub-workflows which allows to extend the pipeline to other methods and tools in future. nf-gwas includes an extensive reporting functionality that allows to inspect thousands of phenotypes and navigate interactive Manhattan plots directly in the web browser.

The pipeline is tested using the unit-style testing framework nf-test and includes a schema definition to run with Nextflow Tower.

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Documentation

Documentation can be found here.

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Citation

Please cite our paper if you use nf-gwas:

Schönherr S, Schachtl-Riess JF, Di Maio S*, Filosi M, Mark M, Lamina C, Fuchsberger C, Kronenberg F, Forer L. Performing highly parallelized and reproducible GWAS analysis on biobank-scale data. NAR Genom Bioinform. 2024 Feb 7;6(1):lqae015. doi: 10.1093/nargab/lqae015. PMID: 38327871; PMCID: PMC10849172.

Quick Start

  1. Install Nextflow (>=22.10.4)

  2. Run the pipeline on a test dataset

nextflow run genepi/nf-gwas -r v1.0.9 -profile test,<docker,singularity,slurm,slurm_with_scratch>

  1. Run the pipeline on your data

nextflow run genepi/nf-gwas -c <nextflow.config> -r v1.0.9 -profile <docker,singularity,slurm,slurm_with_scratch>

Please click here for available test config files.

Development

git clone https://github.com/genepi/nf-gwas cd nf-gwas docker build -t genepi/nf-gwas . # don't ignore the dot nextflow run main.nf -profile test,development

nf-test

nf-gwas makes use of nf-test, a unit-style test framework for Nextflow.

cd nf-gwas curl -fsSL https://code.askimed.com/install/nf-test | bash ./nf-test test

License

nf-gwas is MIT Licensed and was developed at the Institute of Genetic Epidemiology, Medical University of Innsbruck, Austria.

Contact

Owner

  • Name: Institute of Genetic Epidemiology
  • Login: genepi
  • Kind: organization
  • Location: Innsbruck, Austria

Medical University of Innsbruck

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Schönherr"
  given-names: "Sebastian"
- family-names: "Forer"
  given-names: "Lukas"
title: "nf-gwas - A nextflow pipeline to perform GWAS."
version: 0.3.4
url: "https://github.com/genepi/nf-gwas"

GitHub Events

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Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 3
  • Watch event: 6
  • Delete event: 1
  • Issue comment event: 3
  • Push event: 3
  • Pull request event: 6
  • Fork event: 10

Dependencies

.github/workflows/ci-tests.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v2 composite
Dockerfile docker
  • ubuntu 18.04 build
environment.yml pypi
docs/Gemfile rubygems
  • github-pages ~> 219 development
  • jekyll-feed ~> 0.6 development
  • minima ~> 2.0
  • tzinfo ~> 1.2
  • tzinfo-data >= 0
docs/Gemfile.lock rubygems
  • 102 dependencies