nextflow.config

manifest {
    name                                  = 'pre-imputation-qc'
    version                               = '1.3.0'
    description                           = 'A Nextflow pipeline to clean genotyped data and prepare it for genotype imputation on Michigan Imputation Server.'
    author                                = 'Lukas Forer'
    homePage                              = 'https://github.com/lukfor/pre-imputation-qc'
    mainScript                            = 'main.nf'
    nextflowVersion                       = '!>=21.04.0'
}

// Global default params, used in configs
params {

  project = null
  project_date = "`date`"
  input = null
  input_csv = null
  output = "output/genotyped"
  chip = null
  build = null
  strand_file = null
  refalt_file = null

  chunkSize= 20000000
  minSampleCallRate = 0.5
  minSnpCallRate = 0.9
  maf = 0
  hwe = 1E-6
  cleanSampleIds = false
  excludeSamples = null
  useDoubleId = true

  reference = [
    vcf: null
  ]

}

docker.enabled = true
process.container = 'quay.io/genepi/pre-imputation-qc:v1.3.0'

profiles {

    docker {
        docker.enabled                    = true
        docker.userEmulation              = true
        singularity.enabled               = false
    }

    singularity {
        singularity.enabled               = true
        singularity.autoMounts            = true
        docker.enabled                    = false
    }

    development {
        process.container                 = 'genepi/pre-imputation-qc:latest'
        docker.enabled                    = true
        docker.userEmulation              = true
        resume                            = true
        singularity.enabled               = false
    }

}