WES/workflow.wdl

import "./tasks/mapping.wdl" as mapping
import "./tasks/Metrics.wdl" as Metrics
import "./tasks/Dedup.wdl" as Dedup
import "./tasks/deduped_Metrics.wdl" as deduped_Metrics
import "./tasks/Realigner.wdl" as Realigner
import "./tasks/BQSR.wdl" as BQSR
import "./tasks/corealigner.wdl" as corealigner
import "./tasks/PON.wdl" as PON
import "./tasks/TNseq.wdl" as TNseq
import "./tasks/TNscope.wdl" as TNscope
import "./tasks/annovar.wdl" as annovar
import "./tasks/vcf2maf.wdl" as vcf2maf


workflow {{ project_name }} {

	File fastq_1
	File fastq_2
	File? normal_recaled_bam
	File? normal_recaled_bam_index
	String type

	String SENTIEON_INSTALL_DIR
	String SENTIEON_LICENSE
	String sentieon_docker
	String annovar_docker
	String vcf2maf_r_docker
	
	File ref_dir
	String fasta
	File dbmills_dir
	String db_mills
	File dbsnp_dir
	String dbsnp
	File regions
	String disk_size
	String cluster_config

	Boolean set_pon
	File? pon_vcf
	File? cosmic_dir
	String? cosmic_vcf

	Boolean set_annovar
	File? database
	Boolean set_vcf2maf

	call mapping.mapping as mapping {
		input: 
		group=sample + '_' + type,
		sample=sample + '_' + type,
		fastq_1=fastq_1,
		fastq_2=fastq_2,
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		pl="ILLUMINAL",
		fasta=fasta,
		ref_dir=ref_dir,
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call Metrics.Metrics as Metrics {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		sorted_bam=mapping.sorted_bam,
		sorted_bam_index=mapping.sorted_bam_index,
		sample=sample + '_' + type,
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call Dedup.Dedup as Dedup {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		sorted_bam=mapping.sorted_bam,
		sorted_bam_index=mapping.sorted_bam_index,
		sample=sample + '_' + type,
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call deduped_Metrics.deduped_Metrics as deduped_Metrics {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		Dedup_bam=Dedup.Dedup_bam,
		Dedup_bam_index=Dedup.Dedup_bam_index,
		sample=sample + '_' + type,
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call Realigner.Realigner as Realigner {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		Dedup_bam=Dedup.Dedup_bam,
		Dedup_bam_index=Dedup.Dedup_bam_index,
		db_mills=db_mills,
		dbmills_dir=dbmills_dir,
		sample=sample + '_' + type,
		docker=sentieon_docker,
		disk_size=disk_size,
		regions=regions,
		cluster_config=cluster_config
	}

	call BQSR.BQSR as BQSR {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		realigned_bam=Realigner.realigner_bam,
		realigned_bam_index=Realigner.realigner_bam_index,
		db_mills=db_mills,
		dbmills_dir=dbmills_dir,
		dbsnp=dbsnp,
		dbsnp_dir=dbsnp_dir,
		sample=sample + '_' + type,
		regions=regions,
		docker=sentieon_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	if (set_pon && type == "normal") {
		call PON.PON as PON {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			sample=sample,
			fasta=fasta,
			ref_dir=ref_dir,
			normal_recaled_bam=BQSR.recaled_bam,
			normal_recaled_bam_index=BQSR.recaled_bam_index,
			cosmic_vcf=cosmic_vcf,
			cosmic_dir=cosmic_dir,
			dbsnp=dbsnp,
			dbsnp_dir=dbsnp_dir,
			docker=sentieon_docker,
			disk_size=disk_size,
			cluster_config=cluster_config
		}
	}
	
	if (type == "tumor" && defined(normal_recaled_bam)) {
		call corealigner.corealigner as corealigner {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			fasta=fasta,
			ref_dir=ref_dir,
			sample=sample,
			docker=sentieon_docker,
			db_mills=db_mills,
			dbmills_dir=dbmills_dir,
			dbsnp=dbsnp,
			dbsnp_dir=dbsnp_dir,
			tumor_recaled_bam=BQSR.recaled_bam,
			tumor_recaled_bam_index=BQSR.recaled_bam_index,
			normal_recaled_bam=normal_recaled_bam,
			normal_recaled_bam_index=normal_recaled_bam_index,
			disk_size=disk_size,
			cluster_config=cluster_config
		}
		File bam_to_use = corealigner.corealigner_bam
	}

	if (type == "tumor" && !defined(normal_recaled_bam)) {
		File bam_to_use = BQSR.recaled_bam
	}	

	#File bam_to_use = select_first([corealigner.corealigner_bam, BQSR.recaled_bam])


	call TNseq.TNseq as TNseq {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		corealigner_bam=corealigner.corealigner_bam,
		corealigner_bam_index=corealigner.corealigner_bam_index,
		tumor_recaled_bam=BQSR.recaled_bam,
		tumor_recaled_bam_index=BQSR.recaled_bam_index,
		dbsnp=dbsnp,
		dbsnp_dir=dbsnp_dir,
		set_pon=set_pon,
		pon_vcf=pon_vcf,
        cosmic_vcf=cosmic_vcf,
        cosmic_dir=cosmic_dir,
		tumor_name=sample + "_tumor",
		normal_name=sample + "_normal",
		docker=sentieon_docker,
		sample=sample,
		disk_size=disk_size,
		cluster_config=cluster_config
	}
    
	call TNscope.TNscope as TNscope {
		input:
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		fasta=fasta,
		ref_dir=ref_dir,
		corealigner_bam=corealigner.corealigner_bam,
		corealigner_bam_index=corealigner.corealigner_bam_index,
		tumor_recaled_bam=BQSR.recaled_bam,
		tumor_recaled_bam_index=BQSR.recaled_bam_index,
		dbsnp=dbsnp,
		dbsnp_dir=dbsnp_dir,
		set_pon=set_pon,
		pon_vcf=pon_vcf,
        cosmic_vcf=cosmic_vcf,
        cosmic_dir=cosmic_dir,
		tumor_name=sample + "_tumor",
		normal_name=sample + "_normal",
		docker=sentieon_docker,
		sample=sample,
		disk_size=disk_size,
		cluster_config=cluster_config
	}
    
	if (set_annovar && defined(TNscope.TNscope_vcf) && defined(TNseq.TNseq_vcf)){
        call annovar.annovar as annovar {
            input:
            docker=annovar_docker,
            database=database,
            tnscope_vcf_file=TNscope.TNscope_vcf,
            tnseq_vcf_file=TNseq.TNseq_vcf,
            sample=sample,
            cluster_config=cluster_config,
            disk_size=disk_size
        }

    	if (set_vcf2maf){
        	call vcf2maf.vcf2maf as vcf2maf {
            	input:
    	        docker=vcf2maf_r_docker,
        	    multianno_tnscope_txt=annovar.multianno_tnscope_txt,
            	multianno_tnseq_txt=annovar.multianno_tnseq_txt,
    	        sample=sample,
    	        cluster_config=cluster_config,
    	        disk_size=disk_size
    	    }
		}
    }
}