mendelian_concordance/workflow.wdl

import "./tasks/variantsNorm.wdl" as variantsNorm
import "./tasks/mendelian.wdl" as mendelian

workflow {{ project_name }} {
	File inputSamplesFile
	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
	File ref_dir
	String fasta
	String cluster_config
	String disk_size

	scatter (quartet in inputSamples){
		call variantsNorm.variantsNorm as LCL5variantsNorm{
			input:
			vcf=quartet[0],
			ref_dir=ref_dir,
			fasta=fasta,
			sampleName=quartet[4],
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call variantsNorm.variantsNorm as LCL6variantsNorm{
			input:
			vcf=quartet[1],
			ref_dir=ref_dir,
			fasta=fasta,
			sampleName=quartet[5],
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call variantsNorm.variantsNorm as LCL7variantsNorm{
			input:
			vcf=quartet[2],
			ref_dir=ref_dir,
			fasta=fasta,
			sampleName=quartet[6],
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call variantsNorm.variantsNorm as LCL8variantsNorm{
			input:
			vcf=quartet[3],
			ref_dir=ref_dir,
			fasta=fasta,
			sampleName=quartet[7],
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call mendelian.mendelian as LCL5mendelian {
			input:
			child_vcf=LCL5variantsNorm.normed_vcf,
			LCL7_vcf=LCL7variantsNorm.normed_vcf,
			LCL8_vcf=LCL8variantsNorm.normed_vcf,
			LCL7_name=quartet[6],
			LCL8_name=quartet[7],
			child_name=quartet[4],
			ref_dir=ref_dir,
			fasta=fasta,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call mendelian.mendelian as LCL6mendelian {
			input:
			child_vcf=LCL6variantsNorm.normed_vcf,
			LCL7_vcf=LCL7variantsNorm.normed_vcf,
			LCL8_vcf=LCL8variantsNorm.normed_vcf,
			LCL7_name=quartet[6],
			LCL8_name=quartet[7],
			child_name=quartet[5],
			ref_dir=ref_dir,
			fasta=fasta,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
	}
}