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.

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

• 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 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 ...