/pgs-calc-nf

Nextflow pipeline to calculate polygenetic riskscores using pgs-calc

Primary LanguageNextflowMIT LicenseMIT

pgs-calc-nf

nf-test

Nextflow pipeline to calculate polygenic scores using pgs-calc

Requirements

  • Nextflow:
curl -s https://get.nextflow.io | bash
  • Docker

Installation

Build docker image before run the pipeline:

docker build -t lukfor/pgs-calc-nf . # don't ingore the dot here

Test the pipeline and the created docker image with test-data:

nextflow run main.nf \
  --project test-project  \
  --genotypes_imputed "tests/data/*.vcf.gz" \
  --genotypes_imputed_format "vcf" \
  --genotypes_imputed_have_index false \
  --genotypes_build "hg19" \
  --scores "tests/data/*.csv"
  --output output

Normalized score files from PGSCatalog can be downloaded from here.

Contact

Lukas Forer (@lukfor), Institute of Genetic Epidemiology, Medical University of Innsbruck

License

pgs-calc-nf is MIT Licensed.