params {

	//Java options
	
	java_opt_samtofastq = "-Xms3000m"
    java_opt_mergebams = "-Xms6000m"
	java_opt_markdups = "-Xms4000m"
	java_opt_sort = "-Xms4000m"
	java_opt_fix = "-Xms500m"
	java_opt_baserecal = "-Xms4000m"
	java_opt_bqsrreport = "-Xms3000m"
 	java_opt_applybqsr = "-Xms3000m"
    java_opt_gatherbams = "-Xms2000m"
	java_opt_haplotype = "-Xmx4G"
    java_opt_mergevcfs = "-Xmx4G"
    java_opt_genomicsDBimport = "-Xmx4G"


	compression_level = 5
	
	//Reference files
  	fasta = "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta"
  	dbSNP_vcf = "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf"
	known_indels_mills = "s3://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
	known_indels_dbSNP = "s3://broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz"
	axiompoly_vcf =  "s3://broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz"
	hapmap_vcf = "s3://broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz"
	omni_vcf = "s3://broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz"
	onekg_vcf = "s3://broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz"
	sequence_grouping = "s3://<your_s3_bucket>/sequence_grouping.txt"
	sequence_grouping_unmapped = "s3://<your_s3_bucket>/sequence_grouping_with_unmapped.txt"
	scattered_calling_interval = "s3://gatk-test-data/intervals/hg38_wgs_scattered_calling_intervals.txt"

	//Docker images
	gatk_docker = "<gatk:4.1.8.0>"
	gotc_docker = "<genomes-in-the-cloud:2.3.1-1504795437>"
	gatk4110_docker = "<gatk:4.1.1.0>"
	gatk_joint_docker = "<gatk-nightly:2019-05-07-4.1.2.0-5-g53d015e4f-NIGHTLY-SNAPSHOT>"

	//Joint Genotyping options
	callset_name = "test"
	cohort = "test"
	unpadded_intervals_file = "s3://broad-references/hg38/v0/hg38.even.handcurated.20k.intervals"
	eval_interval_list = "s3://broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list"
	snp_recalibration_tranche_values = ["100.0", "99.95", "99.9", "99.8", "99.6", "99.5", "99.4", "99.3", "99.0", "98.0", "97.0", "90.0" ]
	snp_recalibration_annotation_values =  ["QD", "MQRankSum", "ReadPosRankSum", "FS", "MQ", "SOR", "DP"]
	indel_recalibration_annotation_values =  ["FS", "ReadPosRankSum", "MQRankSum", "QD", "SOR", "DP"]
	indel_recalibration_tranche_values = ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"]

}


profiles {

	c5 {
		process.executor = 'awsbatch'
		process.queue = 'NfDemandc5Queue'
	}
	
	c5_spot {
		process.executor = 'awsbatch'
		process.queue = 'NfSpotc5Queue'
	}

	m5 {
		process.executor = 'awsbatch'
		process.queue = 'NfDemandM5Queue'
	}

	m5_spot {
		process.executor = 'awsbatch'
		process.queue = 'NfSpotM5Queue'
	}

	r5 {
		process.executor = 'awsbatch'
		process.queue = 'NfDemandr5Queue'
	}

	r5_spot {
		process.executor = 'awsbatch'
		process.queue = 'NfSpotr5Queue'
	}
}


aws {
    batch {
        cliPath = "/opt/aws-cli/bin/aws"
		maxParallelTransfers = 8
		maxTransferAttempts = 8
    }
}