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

• We track our open tasks using github's issues
• The 1000ft view is located on our Trello board.

• 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+

• 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

  • impute2 from IMPUTE2
  • plink from PLINK 1.9+
  • vcftools from VCFtools
  • bcftoolsfrom bcftools
  • bgzip from htslib
  • eagle from Eagle
  • python2.7

1. Clone this repo
2. Run the "tiny" dataset included

nextflow run imputation.nf -c nextflow.test.tiny.config

3. check for results in outfolder

wc -l output/impute_results/FINAL_VCFS/*

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

3. check for results in outfolder

wc -l output/impute_results/FINAL_VCFS/*

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

2. 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'

3. run with the awsbatch profile

nextflow run imputation.nf -c nextflow.test.small.config -profile awsbatch