mendelian_concordance/workflow.wdl

import "./tasks/mendelian.wdl" as mendelian
import "./tasks/sister.wdl" as sister
import "./tasks/merge.wdl" as merge
 
workflow {{ project_name }} {
	File inputSamplesFile
	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
	File sdf
	String cluster_config
	String disk_size

	scatter (sample in inputSamples){
		call mendelian.mendelian as mendelian {
			input: 
			mother_vcf_gz=sample[0],
			father_vcf_gz=sample[1],
			child_vcf_gz=sample[2],
			mother_vcf_idx=sample[4],
			father_vcf_idx=sample[5],
			child_vcf_idx=sample[6],
			mother_name=sample[8],
			father_name=sample[9],
			child_name=sample[10],
			family_name=sample[11],
			sdf=sdf,
			cluster_config=cluster_config,
			disk_size=disk_size
		}

		call sister.sister as sister {
			input:
			violation_vcf_gz=mendelian.violation_vcf_gz,
			violation_vcf_idx=mendelian.violation_vcf_idx,
			consistent_vcf_gz=mendelian.consistent_vcf_gz,
			consistent_vcf_idx=mendelian.consistent_vcf_idx,
			sister_vcf_gz=sample[3],
			sister_vcf_idx=sample[7],
			sdf=sdf,
			family_name=sample[11],
			cluster_config=cluster_config,
			disk_size=disk_size
		}

	}

	call merge.merge as merge {
		input:
		child_violation_sister=sister.child_violation_sister,
		child_violation_sister_idx=sister.child_violation_sister_idx,
		child_violation_nonsister=sister.child_violation_nonsister,
		child_violation_nonsister_idx=sister.child_violation_nonsister_idx,
		child_consistent_sister=sister.child_consistent_sister,
		child_consistent_sister_idx=sister.child_consistent_sister_idx,
		child_consistent_nonsister=sister.child_consistent_nonsister,
		child_consistent_nonsister_idx=sister.child_consistent_nonsister_idx,
		cluster_config=cluster_config,
		disk_size=disk_size
	}
}