import "./tasks/mapping.wdl" as mapping
import "./tasks/fastqc.wdl" as fastqc
import "./tasks/fastqscreen.wdl" as fastqscreen
import "./tasks/qualimap.wdl" as qualimap
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/TNseq.wdl" as TNseq
import "./tasks/TNscope.wdl" as TNscope


workflow {{ project_name }} {

	File tumor_fastq_1
	File tumor_fastq_2
	File normal_fastq_1
	File normal_fastq_2

	String SENTIEON_INSTALL_DIR
	String SENTIEON_LICENSE
	String sample
	String SENTIEONdocker
	String FASTQCdocker
	String FASTQSCREENdocker
	String QUALIMAPdocker
	
	File screen_ref_dir
	File fastq_screen_conf
	String fasta
	File ref_dir
	File dbmills_dir
	String db_mills
	File dbsnp_dir
	String dbsnp
	String disk_size
	String cluster_config
	


	call mapping.mapping as tumor_mapping {
		input: 
		group=sample + "tumor",
		sample=sample + "tumor",
		fastq_1=tumor_fastq_1,
		fastq_2=tumor_fastq_2,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		pl="ILLUMINAL",
		fasta=fasta,
		ref_dir=ref_dir,
		docker=SENTIEONdocker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}


	call mapping.mapping as normal_mapping {
		input: 
		group=sample + "normal",
		sample=sample + "normal",
		fastq_1=normal_fastq_1,
		fastq_2=normal_fastq_2,
		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
		SENTIEON_LICENSE=SENTIEON_LICENSE,
		pl="ILLUMINAL",
		fasta=fasta,
		ref_dir=ref_dir,
		docker=SENTIEONdocker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call fastqc.fastqc as fastqc {
		input:
		tumor_read1=tumor_fastq_1,
		tumor_read2=tumor_fastq_2,
		normal_read1=normal_fastq_1,
		normal_read2=normal_fastq_2,
		docker=FASTQCdocker,
		cluster_config=cluster_config,
		disk_size=disk_size
	}

	call fastqscreen.fastqscreen as fastqscreen {
		input:
		tumor_read1=tumor_fastq_1,
		tumor_read2=tumor_fastq_2,
		normal_read1=normal_fastq_1,
		normal_read2=normal_fastq_2,
		screen_ref_dir=screen_ref_dir,
		fastq_screen_conf=fastq_screen_conf,
		docker=FASTQSCREENdocker,
		cluster_config=cluster_config,
		disk_size=disk_size
	}


	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 + "tumor",
		docker=SENTIEONdocker,
		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 + "normal",
		docker=SENTIEONdocker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	call qualimap.qualimap as tumor_qualimap {
		input:
		bam=tumor_Dedup.Dedup_bam,
		bai=tumor_Dedup.Dedup_bam_index,
		docker=QUALIMAPdocker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}		

	call qualimap.qualimap as normal_qualimap {
		input:
		bam=normal_Dedup.Dedup_bam,
		bai=normal_Dedup.Dedup_bam_index,
		docker=QUALIMAPdocker,
		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 + "tumor",
		docker=SENTIEONdocker,
		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 + "normal",
		docker=SENTIEONdocker,
		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 + "tumor",
		docker=SENTIEONdocker,
		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 + "normal",
		docker=SENTIEONdocker,
		disk_size=disk_size,
		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_bam=tumor_Realigner.realigner_bam,
		realigned_bam_index=tumor_Realigner.realigner_bam_index,
		db_mills=db_mills,
		dbmills_dir=dbmills_dir,
		dbsnp=dbsnp,
		dbsnp_dir=dbsnp_dir,
		sample=sample + "tumor",
		docker=SENTIEONdocker,
		disk_size=disk_size,
		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_bam=normal_Realigner.realigner_bam,
		realigned_bam_index=normal_Realigner.realigner_bam_index,
		db_mills=db_mills,
		dbmills_dir=dbmills_dir,
		dbsnp=dbsnp,
		dbsnp_dir=dbsnp_dir,
		sample=sample + "normal",
		docker=SENTIEONdocker,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

	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=SENTIEONdocker,
		db_mills=db_mills,
		dbmills_dir=dbmills_dir,
		dbsnp=dbsnp,
		dbsnp_dir=dbsnp_dir,
		disk_size=disk_size,
		tumor_recaled_bam=tumor_BQSR.recaled_bam,
		tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
		normal_recaled_bam=normal_BQSR.recaled_bam,
		normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
		cluster_config=cluster_config
	}

	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,
		dbsnp=dbsnp,
		dbsnp_dir=dbsnp_dir,
		tumor_name=sample + "tumor",
		normal_name=sample + "normal",
		docker=SENTIEONdocker,
		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,
		dbsnp=dbsnp,
		dbsnp_dir=dbsnp_dir,
		tumor_name=sample + "tumor",
		normal_name=sample + "normal",
		docker=SENTIEONdocker,
		sample=sample,
		disk_size=disk_size,
		cluster_config=cluster_config
	}
}