Genotype Imputation Pipeline for H3Africa
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.

Imputation Workflow

This repo contains the workflow which was developed as part of the H3ABioNet Hackathon held in Pretoria, SA in 2016.

Setup (native cluster)


  • Nextflow (can be installed as local user)
  • NXF_HOME needs to be set, and must be in the PATH
  • Note that we've experienced problems running Nextflow when NXF_HOME is on an NFS mount.
  • The Nextflow script also needs to be invoked in a non-NFS folder
  • Java 1.8+

Compute nodes

  • The compute nodes need access to shared storage for input, references, output

  • The following commands need to be available in PATH on the compute nodes

Getting started

Basic test

  1. Clone this repo
  2. Run the "tiny" dataset included
nextflow run -c nextflow.test.tiny.config
  1. check for results in outfolder
wc -l output/impute_results/FINAL_VCFS/*

Larger dataset

  1. Download this slightly larger dataset: small.tar.bz2 and extract into the samples folder
  2. Run this "small" dataset with
nextflow run -c nextflow.test.small.config
  1. check for results in outfolder
wc -l output/impute_results/FINAL_VCFS/*

AWS Batch

This workflow can be run on AWS Batch, an Amazon service that streamlines the running of containerised workflows. Nextflow

  1. Set up the AWS environment. The requirements are:
  • an AWS account with credits. See the AWS grants page for grants
  • a configured Compute Environment and associated AWS Job Queue
  • a configured S3 bucket
  1. Populate the awsbatch profile in
aws.region = 'eu-west-1'
aws.client.storageEncryption = 'AES256'
process.queue = 'large' = 'awsbatch'
executor.awscli = '/home/ec2-user/miniconda/bin/aws'
  1. run with the awsbatch profile
nextflow run -c nextflow.test.small.config -profile awsbatch