high_confidence_calls_intergration/workflow.wdl

import "./tasks/variantsNorm.wdl" as variantsNorm
import "./tasks/sister.wdl" as sister
import "./tasks/mendelian.wdl" as mendelian
import "./tasks/zipIndex.wdl" as zipIndex
import "./tasks/VCFrename.wdl" as VCFrename
import "./tasks/merge.wdl" as merge
 
workflow {{ project_name }} {
	File inputSamplesFile
	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
	File ref_dir
	String fasta
	String cluster_config
	String disk_size
	String mapper_caller

	scatter (sample in inputSamples){
		call variantsNorm.variantsNorm as LCL5variantsNorm{
			input:
			vcf=sample[0],
			ref_dir=ref_dir,
			fasta=fasta,
			sampleName=sample[4],
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call variantsNorm.variantsNorm as LCL6variantsNorm{
			input:
			vcf=sample[1],
			ref_dir=ref_dir,
			fasta=fasta,
			sampleName=sample[5],
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call variantsNorm.variantsNorm as LCL7variantsNorm{
			input:
			vcf=sample[2],
			ref_dir=ref_dir,
			fasta=fasta,
			sampleName=sample[6],
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call variantsNorm.variantsNorm as LCL8variantsNorm{
			input:
			vcf=sample[3],
			ref_dir=ref_dir,
			fasta=fasta,
			sampleName=sample[7],
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call sister.sister as sister{
			input:
			LCL5_vcf=LCL5variantsNorm.normed_vcf,
			LCL6_vcf=LCL6variantsNorm.normed_vcf,
			ref_dir=ref_dir,
			fasta=fasta,
			family_name=sample[8],
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call mendelian.mendelian as mendelian {
			input: 
			sister_vcf=sister.sister_consistent_vcf,
			LCL7_vcf=LCL7variantsNorm.normed_vcf,
			LCL8_vcf=LCL8variantsNorm.normed_vcf,
			LCL7_name=sample[6],
			LCL8_name=sample[7],
			family_name=sample[8],
			ref_dir=ref_dir,
			fasta=fasta,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call zipIndex.zipIndex as zipIndex{
			input:
			mother_vcf=mendelian.mother_vcf,
			father_vcf=mendelian.father_vcf,
			twins_vcf=mendelian.twins_vcf,
			family_name=sample[8],
			cluster_config=cluster_config,
			disk_size=disk_size
		}
		call VCFrename.VCFrename as VCFrename{
			input:
			mother_vcf_gz=zipIndex.mother_vcf_gz,
			father_vcf_gz=zipIndex.father_vcf_gz,
			twins_vcf_gz=zipIndex.twins_vcf_gz,
			mother_vcf_idx=zipIndex.mother_vcf_idx,
			father_vcf_idx=zipIndex.father_vcf_idx,
			twins_vcf_idx=zipIndex.twins_vcf_idx,
			mother_name=sample[7],
			father_name=sample[6],
			family_name=sample[8],
			cluster_config=cluster_config,
			disk_size=disk_size
		}
	}

	call merge.merge as merge {
		input:
		rename_mother_vcf_gz=VCFrename.rename_mother_vcf_gz,
		rename_mother_vcf_idx=VCFrename.rename_mother_vcf_idx,
		rename_father_vcf_gz=VCFrename.rename_father_vcf_gz,
		rename_father_vcf_idx=VCFrename.rename_father_vcf_idx,
		rename_twins_vcf_gz=VCFrename.rename_twins_vcf_gz,
		rename_twins_vcf_idx=VCFrename.rename_twins_vcf_idx,
		mapper_caller=mapper_caller,
		cluster_config=cluster_config,
		disk_size=disk_size
	}
}