Chip imputation evaluation Workflow h3abionet/chipimputation_evaluate_chips

Introduction

The pipeline is to evaluate the imputation performance and accuracy of different arrays starting from sequence data. It masks non tag variants for each array, and then impute to a reference panel using Minimac.
It is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner.
It comes with singularity containers making installation trivial and results highly reproducible.

Documentation

The evaluate_chips pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation and Configuration
2. Configuration for other clusters
3. Running the pipeline

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 to have singularity installed.

• 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, in case of unavailabitity of singularity.

  • minimac4 from MINIMAC4
  • vcftools from VCFtools
  • bcftoolsfrom bcftools
  • bgzip from htslib
  • eagle from Eagle
  • python2.7
  • R with the following packages ...