Genotype Imputation Pipeline for H3Africa
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README.md

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)

Headnode

  • 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 imputation.nf -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 imputation.nf -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'
executor.name = 'awsbatch'
executor.awscli = '/home/ec2-user/miniconda/bin/aws'
  1. run with the awsbatch profile
nextflow run imputation.nf -c nextflow.test.small.config -profile awsbatch