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/bcftools.wdl" as bcftools
#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 inputSamplesFile
	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
	#Array[String] sample

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

	Boolean PONmode
	File? cosmic_dir
	String? cosmic_vcf

	Boolean set_annovar
	Boolean set_vcf2maf
	

	scatter (sample in inputSamples) {
		call mapping.mapping as tumor_mapping {
			input: 
			group=sample[0] + "_tumor",
			sample=sample[0] + "_tumor",
			fastq_1=sample[1],
			fastq_2=sample[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 tumor_Metrics {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			fasta=fasta,
			ref_dir=ref_dir,
			sorted_bam=tumor_mapping.sorted_bam,
			sorted_bam_index=tumor_mapping.sorted_bam_index,
			sample=sample[0] + "_tumor",
			docker=sentieon_docker,
			disk_size=disk_size,
			cluster_config=cluster_config
		}

		call Dedup.Dedup as tumor_Dedup {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			sorted_bam=tumor_mapping.sorted_bam,
			sorted_bam_index=tumor_mapping.sorted_bam_index,
			sample=sample[0] + "_tumor",
			docker=sentieon_docker,
			disk_size=disk_size,
			cluster_config=cluster_config
		}

		call deduped_Metrics.deduped_Metrics as tumor_deduped_Metrics {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			fasta=fasta,
			ref_dir=ref_dir,
			Dedup_bam=tumor_Dedup.Dedup_bam,
			Dedup_bam_index=tumor_Dedup.Dedup_bam_index,
			sample=sample[0] + "_tumor",
			docker=sentieon_docker,
			disk_size=disk_size,
			cluster_config=cluster_config
		}

		call Realigner.Realigner as tumor_Realigner {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			fasta=fasta,
			ref_dir=ref_dir,
			Dedup_bam=tumor_Dedup.Dedup_bam,
			Dedup_bam_index=tumor_Dedup.Dedup_bam_index,
			db_mills=db_mills,
			dbmills_dir=dbmills_dir,
			sample=sample[0] + "_tumor",
			docker=sentieon_docker,
			disk_size=disk_size,
			regions=regions,
			cluster_config=cluster_config
		}

		call BQSR.BQSR as tumor_BQSR {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			fasta=fasta,
			ref_dir=ref_dir,
			realigned_bam1=tumor_Realigner.realigner_bam,
			realigned_bam_index1=tumor_Realigner.realigner_bam_index,
			db_mills=db_mills,
			dbmills_dir=dbmills_dir,
			dbsnp=dbsnp,
			dbsnp_dir=dbsnp_dir,
			sample=sample[0] + "_tumor",
			regions=regions,
			docker=sentieon_docker,
			disk_size=disk_size,
			cluster_config=cluster_config
		}
	}

	scatter (sample in inputSamples) {	
		call mapping.mapping as normal_mapping {
			input: 
			group=sample[0] + "_normal",
			sample=sample[0] + "_normal",
			fastq_1=sample[3],
			fastq_2=sample[4],
			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 normal_Metrics {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			fasta=fasta,
			ref_dir=ref_dir,
			sorted_bam=normal_mapping.sorted_bam,
			sorted_bam_index=normal_mapping.sorted_bam_index,
			sample=sample[0] + "_normal",
			docker=sentieon_docker,
			disk_size=disk_size,
			cluster_config=cluster_config
		}

		call Dedup.Dedup as normal_Dedup {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			sorted_bam=normal_mapping.sorted_bam,
			sorted_bam_index=normal_mapping.sorted_bam_index,
			sample=sample[0] + "_normal",
			docker=sentieon_docker,
			disk_size=disk_size,
			cluster_config=cluster_config
		}

		call deduped_Metrics.deduped_Metrics as normal_deduped_Metrics {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			fasta=fasta,
			ref_dir=ref_dir,
			Dedup_bam=normal_Dedup.Dedup_bam,
			Dedup_bam_index=normal_Dedup.Dedup_bam_index,
			sample=sample[0] + "_normal",
			docker=sentieon_docker,
			disk_size=disk_size,
			cluster_config=cluster_config
		}

		call Realigner.Realigner as normal_Realigner {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			fasta=fasta,
			ref_dir=ref_dir,
			Dedup_bam=normal_Dedup.Dedup_bam,
			Dedup_bam_index=normal_Dedup.Dedup_bam_index,
			db_mills=db_mills,
			dbmills_dir=dbmills_dir,
			sample=sample[0] + "_normal",
			docker=sentieon_docker,
			disk_size=disk_size,
			regions=regions,
			cluster_config=cluster_config
		}

		call BQSR.BQSR as normal_BQSR {
			input:
			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
			SENTIEON_LICENSE=SENTIEON_LICENSE,
			fasta=fasta,
			ref_dir=ref_dir,
			realigned_bam1=normal_Realigner.realigner_bam,
			realigned_bam_index1=normal_Realigner.realigner_bam_index,
			db_mills=db_mills,
			dbmills_dir=dbmills_dir,
			dbsnp=dbsnp,
			dbsnp_dir=dbsnp_dir,
			sample=sample[0] + "_normal",
			regions=regions,
			docker=sentieon_docker,
			disk_size=disk_size,
			cluster_config=cluster_config
		}

		if (PONmode) {
			call PON.PON as PON {
				input:
				SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
				SENTIEON_LICENSE=SENTIEON_LICENSE,
				sample=sample[0],
				fasta=fasta,
				ref_dir=ref_dir,
				normal_recaled_bam=normal_BQSR.recaled_bam,
				normal_recaled_bam_index=normal_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
			}
		}
		File pon_vcf=PON.pon_vcf
	}

	call bcftools.bcftools as bcftools {
		input:
		PONmode=PONmode,
		pon_vcf=pon_vcf,
		docker=bcftools_docker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}
	
}