import "./tasks/mendelian.wdl" as mendelian
import "./tasks/merge_mendelian.wdl" as merge_mendelian
import "./tasks/count_mendelian.wdl" as count_mendelian

workflow {{ project_name }} {
	File family_vcf
	File ref_dir
	File vote_summary
	String fasta
	String MENDELIANdocker
	String DIYdocker
	String BIGcluster_config
	String SMALLcluster_config
	String disk_size

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

	call count_mendelian.count_mendelian as count_mendelian {
		input:
		project_mendelian=merge_mendelian.project_mendelian,
		vote_summary=vote_summary,
		family_vcf=family_vcf,
		docker=DIYdocker,
		cluster_config=SMALLcluster_config,
		disk_size=disk_size
	}
}