quartet_wes_vcf/workflow.wdl

import "./tasks/rename_vcf.wdl" as rename_vcf
import "./tasks/benchmark.wdl" as benchmark
import "./tasks/multiqc.wdl" as multiqc
import "./tasks/multiqc_hap.wdl" as multiqc_hap
import "./tasks/extract_tables.wdl" as extract_tables
import "./tasks/extract_tables_vcf.wdl" as extract_tables_vcf
import "./tasks/mendelian.wdl" as mendelian
import "./tasks/merge_mendelian.wdl" as merge_mendelian
import "./tasks/merge_family.wdl" as merge_family
import "./tasks/filter_vcf.wdl" as filter_vcf


workflow {{ project_name }} {

	File? vcf_D5
	File? vcf_D6
	File? vcf_F7
	File? vcf_M8

	File bed

	String BENCHMARKdocker
	String MENDELIANdocker
	String DIYdocker
	String MULTIQCdocker
	String BEDTOOLSdocker

	String fasta
	File ref_dir
	File dbmills_dir
	String db_mills
	File dbsnp_dir
	String dbsnp
	String pl
	File reference_bed_dict

	File screen_ref_dir
	File fastq_screen_conf
	File benchmarking_dir
	File benchmark_region

	String project

	String disk_size
	String BIGcluster_config
	String SMALLcluster_config

	if (vcf_D5!= "") {
		call rename_vcf.rename_vcf as rename_vcf{
			input:
			vcf_D5=vcf_D5,
			vcf_D6=vcf_D6,
			vcf_F7=vcf_F7,
			vcf_M8=vcf_M8,
			project=project,
			docker=DIYdocker,
			cluster_config=SMALLcluster_config,
			disk_size=disk_size
		}
		call filter_vcf.filter_vcf as filter_vcf_D5_vcf {
			input:
			vcf=rename_vcf.vcf_D5_renamed,
			bed=bed,
			benchmark_region=benchmark_region,
			project=project,
			docker=BEDTOOLSdocker,
			cluster_config=SMALLcluster_config,
			disk_size=disk_size
		}

		call benchmark.benchmark as benchmark_D5_vcf {
			input:
			filtered_vcf=filter_vcf_D5_vcf.filtered_vcf,
			bed=filter_vcf_D5_vcf.filtered_bed,
			benchmarking_dir=benchmarking_dir,
			ref_dir=ref_dir,
			fasta=fasta,
			docker=BENCHMARKdocker,
			cluster_config=BIGcluster_config,
			disk_size=disk_size
		}

		call filter_vcf.filter_vcf as filter_vcf_D6_vcf {
			input:
			vcf=rename_vcf.vcf_D6_renamed,
			docker=BEDTOOLSdocker,
			bed=bed,
			benchmark_region=benchmark_region,
			project=project,
			cluster_config=SMALLcluster_config,
			disk_size=disk_size			
		}

		call benchmark.benchmark as benchmark_D6_vcf {
			input:
			filtered_vcf=filter_vcf_D6_vcf.filtered_vcf,
			bed=filter_vcf_D6_vcf.filtered_bed,
			benchmarking_dir=benchmarking_dir,
			ref_dir=ref_dir,
			fasta=fasta,
			docker=BENCHMARKdocker,
			cluster_config=BIGcluster_config,
			disk_size=disk_size
		}

		call filter_vcf.filter_vcf as filter_vcf_F7_vcf {
			input:
			vcf=rename_vcf.vcf_F7_renamed,
			docker=BEDTOOLSdocker,
			bed=bed,
			benchmark_region=benchmark_region,
			project=project,
			cluster_config=SMALLcluster_config,
			disk_size=disk_size			
		}

		call benchmark.benchmark as benchmark_F7_vcf {
			input:
			filtered_vcf=filter_vcf_F7_vcf.filtered_vcf,
			bed=filter_vcf_F7_vcf.filtered_bed,
			benchmarking_dir=benchmarking_dir,
			ref_dir=ref_dir,
			fasta=fasta,
			docker=BENCHMARKdocker,
			cluster_config=BIGcluster_config,
			disk_size=disk_size
		}

		call filter_vcf.filter_vcf as filter_vcf_M8_vcf {
			input:
			vcf=rename_vcf.vcf_M8_renamed,
			docker=BEDTOOLSdocker,
			bed=bed,
			benchmark_region=benchmark_region,
			project=project,
			cluster_config=SMALLcluster_config,
			disk_size=disk_size			
		}

		call benchmark.benchmark as benchmark_M8_vcf {
			input:
			filtered_vcf=filter_vcf_M8_vcf.filtered_vcf,
			bed=filter_vcf_M8_vcf.filtered_bed,
			benchmarking_dir=benchmarking_dir,
			ref_dir=ref_dir,
			fasta=fasta,
			docker=BENCHMARKdocker,
			cluster_config=BIGcluster_config,
			disk_size=disk_size
		}

	    Array[File] benchmark_summary_hap = [benchmark_D5_vcf.summary, benchmark_D6_vcf.summary, benchmark_F7_vcf.summary, benchmark_M8_vcf.summary]

		call multiqc_hap.multiqc_hap as multiqc_hap {
			input:
			summary=benchmark_summary_hap,
			docker=MULTIQCdocker,
			cluster_config=SMALLcluster_config,
			disk_size=disk_size
		}

		call extract_tables_vcf.extract_tables_vcf as extract_tables_vcf {
			input:
			hap=multiqc_hap.hap,
			project=project,
			docker=DIYdocker,
			cluster_config=SMALLcluster_config,
			disk_size=disk_size
		}

		call merge_family.merge_family as merge_family_vcf {
			input:
			D5_vcf=benchmark_D5_vcf.rtg_vcf,
			D6_vcf=benchmark_D6_vcf.rtg_vcf,
			F7_vcf=benchmark_F7_vcf.rtg_vcf,
			M8_vcf=benchmark_M8_vcf.rtg_vcf,
			D5_vcf_tbi=benchmark_D5_vcf.rtg_vcf_index,
			D6_vcf_tbi=benchmark_D6_vcf.rtg_vcf_index,
			F7_vcf_tbi=benchmark_F7_vcf.rtg_vcf_index,
			M8_vcf_tbi=benchmark_M8_vcf.rtg_vcf_index,
			project=project,
			docker=BENCHMARKdocker,
			cluster_config=SMALLcluster_config,
			disk_size=disk_size,
		}

		call mendelian.mendelian as mendelian_vcf {
			input:
			family_vcf=merge_family_vcf.family_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_vcf {
			input:
			D5_trio_vcf=mendelian_vcf.D5_trio_vcf,
			D6_trio_vcf=mendelian_vcf.D6_trio_vcf,
			family_vcf=merge_family_vcf.family_vcf,
			docker=DIYdocker,
			cluster_config=SMALLcluster_config,
			disk_size=disk_size
		}
	}
}