nextflow.config

process.cache = 'deep'

nextflowVersion = '>=23.0'

import java.time.*
Date now = new Date()


params {
    day                = now.format("yyyMMdd")
    timestamp          = now.format("yyyyMMdd-HH-mm-ss")
    out                = "Analysis_Results-${day}"
    help = false
    debug = false
    download_vcf = false
    finemap = true
    fix = true
    maf = 0.05
    sparse_cut = 0.05
    group_qtl = 1000
    ci_size = 150
    pca = false
    mapping = true
    matrix = false
    simulation = false
    species = "c_elegans"
    mediation = false

    simulate_maf      = "all_species/simulate_maf.csv"
    simulate_nqtl     = "all_species/simulate_nqtl.csv"
    simulate_reps     = 2
    simulate_h2       = "all_species/simulate_h2.csv"
    simulate_eff      = "all_species/simulate_effect_sizes.csv"
    simulate_strains  = "all_species/simulate_strains.tsv"
    simulate_qtlloc   = null
    sthresh = "BF"
}

profiles {
    standard { includeConfig 'conf/rockfish.config' }
    rockfish { includeConfig 'conf/rockfish.config' }
    gcp { includeConfig 'conf/gcp.config' }
    quest { includeConfig 'conf/quest.config' }
    local { includeConfig 'conf/local.config' }
}

report {
    enabled = true
    file = "${params.out}/${params.timestamp}_report.html"
}

timeline {
    enabled = true
    file = "${params.out}/${params.timestamp}_timeline.html"
}

process {
    container = 'andersenlab/nemascan:20220407173056db3227'
    //container = 'msauria/nemascan:060724'

    withLabel: R {
        container = 'andersenlab/r_packages:v0.7'
    }

    withLabel: mediation {
        container = 'andersenlab/mediation:20220407173046db3227'
    }

    withLabel: prep_sims {
        container = 'mckeowr1/prep_sims:1.1'
    }

    withLabel: gcta {
        container = 'andersenlab/gcta:060624'
    }

    withLabel: assess_sims {
        container = 'mckeowr1/asess_sims:1.1'
    }
}