main.nf

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2

import org.yaml.snakeyaml.Yaml

// Misc Parameters
params.VERBOSITY = 0
params.TRAITS_DATASET = "You need to provide a Traits dataset."
params.UKB_ENCODING_FILE = "NO_UKB_ENCODING_FILE"
params.CALL_THRESHOLD = 0.9
params.POSITIVITY_CONSTRAINT = 0.01
params.MAF_THRESHOLD = 0.01
params.COHORT = "UKB"
params.UKB_CONFIG = "${projectDir}/assets/ukbconfig.yaml"
params.UKB_WITHDRAWAL_LIST = "${projectDir}/assets/NO_WITHDRAWAL_LIST"
params.OUTDIR = "${launchDir}/results"

// Confounding adjustment by PCA
params.NB_PCS = 6
params.QC_FILE = "${projectDir}/assets/NO_QC_FILE"
params.LD_BLOCKS = "${projectDir}/assets/NO_LD_BLOCKS"
params.FLASHPCA_EXCLUSION_REGIONS = "${projectDir}/assets/exclusion_regions_hg19.txt"

// Estimands Generation 
params.BATCH_SIZE = 50

// CUSTOM
params.ESTIMANDS_CONFIG = "NO_ESTIMANDS_CONFIG"

// SVP Parameters
params.SVP = false
params.GRM_NSPLITS = 100
params.NB_SVP_ESTIMATORS = 100
params.MAX_SVP_THRESHOLD = 0.9
params.ESTIMATOR_KEY = "1"

// TMLE Parameters
params.KEEP_IC = params.SVP == true ? true : false
params.PVAL_THRESHOLD = 0.05
params.TL_SAVE_EVERY = params.BATCH_SIZE
params.ESTIMATORS_CONFIG = "wtmle-ose--tunedxgboost"

// Simulations
params.TRAIN_RATIO = 6
params.SAMPLE_GA_HITS = true
params.GA_MAX_VARIANTS = 50
params.GA_DISTANCE_THRESHOLD = 1000000
params.GA_PVAL_THRESHOLD = 1e-5
params.GA_MAF_THRESHOLD = 0.01
params.N_REPEATS = 2
params.RNGS = 1..250
params.SAMPLE_SIZES = [500000]
params.GA_TRAIT_TABLE = "${projectDir}/assets/Traits_Table_GeneATLAS.csv"
params.MIN_FACTOR_LEVEL_OCCURENCES = 10
params.MAX_SAMPLING_ATTEMPTS = 1000
params.NSAMPLES_FOR_TRUTH = 1000000

include { GWAS } from './workflows/gwas.nf'
include { TARGENE } from './workflows/targene.nf'
include { PCA } from './workflows/pca.nf'
include { MAKE_DATASET } from './workflows/dataset.nf'
include { NULL_SIMULATION; REALISTIC_SIMULATION } from './workflows/simulations.nf'

def isGWAS(){
    config = new Yaml().load(new FileReader(params.ESTIMANDS_CONFIG))
    return config.type == 'gwas'
}

log.info """\
         ${workflow.manifest.name} v${workflow.manifest.version}
         ==========================
         Cohort Type  : ${params.COHORT}
         --
         run as       : ${workflow.commandLine}
         started at   : ${workflow.start}
         config files : ${workflow.configFiles}
         container    : ${workflow.containerEngine}
         ==========================
         """
         .stripIndent()


workflow  {
    if (isGWAS()) {
        GWAS()
    }
    else {
        TARGENE()
    }
}