quartet-wes-germline-data-analysis-qc/workflow.wdl

import "./tasks/benchmark.wdl" as benchmark
import "./tasks/mendelian.wdl" as mendelian
import "./tasks/merge_mendelian.wdl" as merge_mendelian
import "./tasks/merge_family.wdl" as merge_family
import "./tasks/quartet_mendelian.wdl" as quartet_mendelian


workflow {{ project_name }} {

	File LCL5_1
	File LCL6_1
	File LCL7_1
	File LCL8_1

	File LCL5_2
	File LCL6_2
	File LCL7_2
	File LCL8_2

	File LCL5_3
	File LCL6_3
	File LCL7_3
	File LCL8_3

	String BENCHMARKdocker
	String MENDELIANdocker
	String DIYdocker


	String fasta
	File ref_dir

	File benchmarking_dir

	String project

	String disk_size
	String BIGcluster_config
	String SMALLcluster_config

	call benchmark.benchmark as LCL5_1_benchmark {
		input:
		vcf=LCL5_1,
		benchmarking_dir=benchmarking_dir,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}

	call benchmark.benchmark as LCL5_2_benchmark {
		input:
		vcf=LCL5_2,
		benchmarking_dir=benchmarking_dir,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}

	call benchmark.benchmark as LCL5_3_benchmark {
		input:
		vcf=LCL5_3,
		benchmarking_dir=benchmarking_dir,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}

	call benchmark.benchmark as LCL6_1_benchmark {
		input:
		vcf=LCL6_1,
		benchmarking_dir=benchmarking_dir,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}

	call benchmark.benchmark as LCL6_2_benchmark {
		input:
		vcf=LCL6_2,
		benchmarking_dir=benchmarking_dir,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}

	call benchmark.benchmark as LCL6_3_benchmark {
		input:
		vcf=LCL6_3,
		benchmarking_dir=benchmarking_dir,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}

	call benchmark.benchmark as LCL7_1_benchmark {
		input:
		vcf=LCL7_1,
		benchmarking_dir=benchmarking_dir,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}	

	call benchmark.benchmark as LCL7_2_benchmark {
		input:
		vcf=LCL7_2,
		benchmarking_dir=benchmarking_dir,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}	

	call benchmark.benchmark as LCL7_3_benchmark {
		input:
		vcf=LCL7_3,
		benchmarking_dir=benchmarking_dir,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}	


	call benchmark.benchmark as LCL8_1_benchmark {
		input:
		vcf=LCL8_1,
		benchmarking_dir=benchmarking_dir,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}

	call benchmark.benchmark as LCL8_2_benchmark {
		input:
		vcf=LCL8_2,
		benchmarking_dir=benchmarking_dir,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}

	call benchmark.benchmark as LCL8_3_benchmark {
		input:
		vcf=LCL8_3,
		benchmarking_dir=benchmarking_dir,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}

	call merge_family.merge_family as merge_family_1 {
		input:
		LCL5_vcf_gz=LCL5_1_benchmark.rtg_vcf,
		LCL5_vcf_idx=LCL5_1_benchmark.rtg_vcf_index,
		LCL6_vcf_gz=LCL6_1_benchmark.rtg_vcf,
		LCL6_vcf_idx=LCL6_1_benchmark.rtg_vcf_index,
		LCL7_vcf_gz=LCL7_1_benchmark.rtg_vcf,
		LCL7_vcf_idx=LCL7_1_benchmark.rtg_vcf_index,
		LCL8_vcf_gz=LCL8_1_benchmark.rtg_vcf,
		LCL8_vcf_idx=LCL8_1_benchmark.rtg_vcf,
		project=project,
		rep="1",
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}

	call merge_family.merge_family as merge_family_2 {
		input:
		LCL5_vcf_gz=LCL5_2_benchmark.rtg_vcf,
		LCL5_vcf_idx=LCL5_2_benchmark.rtg_vcf_index,
		LCL6_vcf_gz=LCL6_2_benchmark.rtg_vcf,
		LCL6_vcf_idx=LCL6_2_benchmark.rtg_vcf_index,
		LCL7_vcf_gz=LCL7_2_benchmark.rtg_vcf,
		LCL7_vcf_idx=LCL7_2_benchmark.rtg_vcf_index,
		LCL8_vcf_gz=LCL8_2_benchmark.rtg_vcf,
		LCL8_vcf_idx=LCL8_2_benchmark.rtg_vcf,
		project=project,
		rep="2",
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}

	call merge_family.merge_family as merge_family_3 {
		input:
		LCL5_vcf_gz=LCL5_3_benchmark.rtg_vcf,
		LCL5_vcf_idx=LCL5_3_benchmark.rtg_vcf_index,
		LCL6_vcf_gz=LCL6_3_benchmark.rtg_vcf,
		LCL6_vcf_idx=LCL6_3_benchmark.rtg_vcf_index,
		LCL7_vcf_gz=LCL7_3_benchmark.rtg_vcf,
		LCL7_vcf_idx=LCL7_3_benchmark.rtg_vcf_index,
		LCL8_vcf_gz=LCL8_3_benchmark.rtg_vcf,
		LCL8_vcf_idx=LCL8_3_benchmark.rtg_vcf,
		project=project,
		rep="3",
		docker=BENCHMARKdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size,
	}

	call mendelian.mendelian as mendelian_1 {
		input:
		family_vcf=merge_family_1.merged_vcf,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=MENDELIANdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size		
	}

	call mendelian.mendelian as mendelian_2 {
		input:
		family_vcf=merge_family_2.merged_vcf,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=MENDELIANdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size		
	}

	call mendelian.mendelian as mendelian_3 {
		input:
		family_vcf=merge_family_3.merged_vcf,
		ref_dir=ref_dir,
		fasta=fasta,
		docker=MENDELIANdocker,
		cluster_config=BIGcluster_config,
		disk_size=disk_size		
	}

	call merge_mendelian.merge_mendelian as merge_mendelian_1 {
		input:
		D5_trio_vcf=mendelian_1.D5_trio_vcf,
		D6_trio_vcf=mendelian_1.D6_trio_vcf,
		family_vcf=merge_family_1.merged_vcf,
		docker=DIYdocker,
		cluster_config=SMALLcluster_config,
		disk_size=disk_size
	}

	call merge_mendelian.merge_mendelian as merge_mendelian_2 {
		input:
		D5_trio_vcf=mendelian_2.D5_trio_vcf,
		D6_trio_vcf=mendelian_2.D6_trio_vcf,
		family_vcf=merge_family_2.merged_vcf,
		docker=DIYdocker,
		cluster_config=SMALLcluster_config,
		disk_size=disk_size
	}

	call merge_mendelian.merge_mendelian as merge_mendelian_3 {
		input:
		D5_trio_vcf=mendelian_3.D5_trio_vcf,
		D6_trio_vcf=mendelian_3.D6_trio_vcf,
		family_vcf=merge_family_3.merged_vcf,
		docker=DIYdocker,
		cluster_config=SMALLcluster_config,
		disk_size=disk_size
	}

	call quartet_mendelian.quartet_mendelian as quartet_mendelian{
		input:
		summary_1=merge_mendelian_1.project_mendelian_summary,
		summary_2=merge_mendelian_2.project_mendelian_summary,
		summary_3=merge_mendelian_3.project_mendelian_summary,
		LCL5_hap_1=LCL5_1_benchmark.summary,
		LCL5_hap_2=LCL5_2_benchmark.summary,
		LCL5_hap_3=LCL5_3_benchmark.summary,
		LCL6_hap_1=LCL6_1_benchmark.summary,
		LCL6_hap_2=LCL6_2_benchmark.summary,
		LCL6_hap_3=LCL6_3_benchmark.summary,
		LCL7_hap_1=LCL7_1_benchmark.summary,
		LCL7_hap_2=LCL7_2_benchmark.summary,
		LCL7_hap_3=LCL7_3_benchmark.summary,	
		LCL8_hap_1=LCL8_1_benchmark.summary,
		LCL8_hap_2=LCL8_2_benchmark.summary,
		LCL8_hap_3=LCL8_3_benchmark.summary,
		docker=DIYdocker,
		project=project,
		cluster_config=SMALLcluster_config,
		disk_size=disk_size
	}

}