Nextflow script to create the imputation
A portable, scalable snp imputation pipeline implemented in Nextflow.
The pipeline is built on Nextflow as a workflow engine, so it needs to be installed first:
curl -fsSL get.nextflow.io | bash
With Nextflow installed, the easiest way to use the pipeline is to use the prepared Docker container which contains all external dependencies.
docker pull insilicodb/docker-impute2
The imputation pipeline needs reference data this can be found on the Impute2 website. The reference data the pipeline is tested with is here.
Here's how to start an example run using Docker (using the example dataset and parameterization included in the distribution):
$ nextflow run insilicodb/snp-imputation-nf --pedFile <pedFile> --mapFile <mapFile> --genticMapDir <referenceDataDir>
For your own runs, provide your own file names, paths, parameters, etc. as defined in the nextflow.config file.