nextflow.config

includeConfig "${projectDir}/configs/profileSelector.nf"


params {

	// General
	inputDir = "/home/kesoh/esoh/geneMap/elvis/haploanalysis/"
	outputDir = "/home/kesoh/esoh/geneMap/elvis/haploanalysis/output/"
	outPrefix = "gh-wes"
	vcf = "gh-kgp.hapdata.vcf.gz"														// must be found in the input directory

	// Mutation age
	variantName = "r143w" 																		// this should be any name of your choosing
	variantId = "rs80338948"																	// if the rsid is not present, provide the ID recorded in the VCF file, e.g. 11:5248232
	sampleIdsOfAffectedPopulation = "unrelatedSamplesHomozygousForR143W.affected.txt"				// must be found in the input director
	sampleIdsOfUnaffectedPopulation = "unrelatedSamplesNegativeForR143W.unaffected.txt"			// must be found in the input director
	chromosomeNumber = 13
	leastLDbetweenTags = 0.1 																	// lowest linkage disequilibrium threshold between tag variants (0.022)
	mutationRegionSize = 2000000 																// total distance to span the mutation upstream and downstream (0.00024)
	popGrowthRate = 0.022
	variantAlleleFreq = 0.00024
	burnIterations = 1000000
	mainIterations = 1000000
	numberOfSimultaneousRuns = 10 																// this is also called number of chains

    // Haplotype Analysis
	hapSamplesDir = "${projectDir}/hapsamples/"													// contains ALL (and ONLY) '.txt' files of samples analyze in vcfFile. One '.txt' file per population (e.g. LWK.txt, CEU.txt, JPT.txt, mypop.txt)
	snpList = "/home/kesoh/esoh/geneMap/elvis/mutationAge/output/r143w-snps.list"

}