impute_with_onephased_prephasing.config

params {

    work_dir = "/$PWD" 
    output_dir = "./output/imputation"

    input_dir = "./output/qc"
    input_pat = "test-nd-c-c"
    
    chromosomes_List = [21,22]
    chromosomeSizesFile = "./hg19_chromosomes_size/hg19_chromosomes_size.txt"

    map_dir = "./impute_ref/1000GP_Phase3/"
    map_pattern = "genetic_map_chr%s_combined_b37.txt"

    ref_panel_dir = "./impute_ref/1000GP_Phase3/"
    ref_hap_pattern = "1000GP_Phase3_chr%s.hap.gz"
    ref_leg_pattern = "1000GP_Phase3_chr%s.legend.gz"
    ref_sample = "1000GP_Phase3.sample"

    maxForks_shapeit = 10
    maxForks_impute2 = 20

}

// process {
//     executor='sge'
//     queue='main.q'
//     clusterOptions = '-V -S /bin/bash'
// }

timeline { 
    enabled=true
    file = "${params.output_dir}/${params.input_pat}_timeline.html"
}

report {
    enabled = true
    file = "${params.output_dir}/${params.input_pat}_runtime.html"
}