README.md

nf-imputationserver-panels

This repository includes a Nextflow pipeline to shuffle reference panels and compress it as msav files for Minimac4. It works with all data formats rand-recom supports (tested with vcf.gz, bcf).

Getting started

git clone https://github.com/seppinho/imputation-panels
docker build -t genepi/imputation-panels .
nextflow run main.nf -c tests/test_three_vcfs.config -profile development

Profiles

We also provide profiles for docker, singularity and slurm in case you don't want to build the image locally.

nextflow run main.nf -c tests/test_three_vcfs.config -profile docker

Sample Config

params {
    project = "three_vcfs"
    files   = "tests/input/three/*.vcf.gz"
    target_length = 20000000
}

Final msav data is written to output/${params.project}.