nf-neestimator

A nextflow pipeline for Ne estimates with bootstrapping

Background

This pipeline is an attempt to call NeEstimator2 by bootstrapping individuals from a plink binary file. You require both nextflow and singularity (or docker) configured in order to call this pipeline properly

Calling pipeline

Simply type:

nextflow run cnr-ibba/nf-neestimator -resume -profile singularity --prefix <plink file prefix>

where the --prefix parameter is the same prefix you would pass as plink --bfile

Customize configuration

This pipeline is configured for bootstrapping 10, 20 and 100 individuals 1000 times. If you need to customize the bootstrapping, you can create a custom configuration file like this:

params {
    prefix      = '<plink file prefix>'
    steps       = 50
    individuals = [10, 20, 30]
}

Add then provide this custom configuration file with the nextflow -config parameter. See configuration file in the nexflow documentation for more information