nextflow.config

manifest {
    name                                  = 'imputationserver'
    version                               = 'v2.0.0-beta5'
    description                           = 'Genotype Imputation Pipeline'
    author                                = 'Lukas Forer & Sebastian Schönherr'
    homePage                              = 'https://github.com/genepi/nf-imputationserver'
    mainScript                            = 'main.nf'
    nextflowVersion                       = '!>=21.04.0'
}

// Global default params, used in configs
params {

    project                = null
    project_date           = "`date`"
    files                  = null    
    population             = null
    refpanel_yaml          = null

    mode                   = 'imputation'
    chunksize              = 20000000
    min_samples            = 20
    max_samples            = 50000
    merge_results          = true
    password               = null
    send_mail              = false

    service = [
        name: "Michigan Imputation Server",
        email: null,
        url : null
    ]

    user = [
        name: null,
        email: null
    ]
    
    phasing = [ 
        engine: 'eagle',
        window: 5000000
    ]

    imputation = [ 
        enabled: true,
        window: 500000,
        minimac_min_ratio: 0.00001,
        min_r2: 0,  
        meta: false,
        md5: false, 
        create_index: false,
        decay: 0   
    ]

    encryption = [
        enabled: true,
        aes: false
    ]

    ancestry = [ 
        enabled: false,
        dim: 10,
        dim_high: 20,
        batch_size: 50,
        reference: null,
        max_pcs: 8,
        k: 10,
        threshold: 0.75
    ]

    pgs = [ 
        enabled: false,
        min_r2: 0,
        fix_strand_flips: false,
        category: "all"
    ]

    pgscatalog = [
        scores: "",
        meta: ""
    ]

}

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

profiles {
    debug { process.beforeScript          = 'echo $HOSTNAME' }

    process.container                 = 'quay.io/genepi/imputation-docker:v0.3.0'

    test  {
         includeConfig 'conf/test.config'
    }
        
    development {
        process.container                 = 'genepi/imputation-docker:latest'
        docker.enabled                    = true
        resume                            = true
        singularity.enabled               = false
    }

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

    singularity {
        singularity.enabled               = true
        singularity.autoMounts            = true
        docker.enabled                    = false
    }
    
    slurm {
        process.executor                  = 'slurm'
        singularity.enabled               = true
        singularity.autoMounts            = true
        docker.enabled                    = false
    }
    

   test {
        includeConfig 'conf/test.config'
   }

}