test12

tasks/BQSR.wdl

 	command <<<
 		set -o pipefail
 		set -e
-		gatk BaseRecalibrator \
+		/usr/local/gatk-4.4.0.0/gatk BaseRecalibrator \
 				-R ${ref_dir}/${fasta} \ 
 				-I ${realigned_bam} \
 				--known-sites ${dbsnp_dir}/${dbsnp}	\
 				--known-sites ${dbmills_dir}/${db_mills} \
 				-O ${sample}_recal_data.table
-		
-		gatk ApplyBQSR \
+		/usr/local/gatk-4.4.0.0/gatk ApplyBQSR \
 				-R ${ref_dir}/${fasta} \
 				-I ${realigned_bam} \
 				-bqsr ${sample}_recal_data.table \
 				-O ${sample}.sorted.deduped.realigned.recaled.bam
-		
-		samtools index -@ $(nproc) -o  ${sample}.sorted.deduped.realigned.recaled.bam.bai  ${sample}.sorted.deduped.realigned.recaled.bam
+		/usr/local/samtools-1.17/bin/samtools index -@ $(nproc) -o  ${sample}.sorted.deduped.realigned.recaled.bam.bai  ${sample}.sorted.deduped.realigned.recaled.bam
 	>>>
 	runtime {
 		docker:docker

tasks/Dedup.wdl

 					-M ${sample}_dedup_metrics.txt \
 					--REMOVE_DUPLICATES
 					
-		samtools index -@ $(nproc) -o  ${sample}.sorted.deduped.bam.bai  ${sample}.sorted.deduped.bam
+		/usr/local/samtools-1.17/bin/samtools index -@ $(nproc) -o  ${sample}.sorted.deduped.bam.bai  ${sample}.sorted.deduped.bam
 	>>>
 	runtime {
 		docker:docker

workflow.wdl

 			disk_size=disk_size
 		}		
 
-		call mapping.mapping as mapping_D6 {
-			input: 
-			pl=pl,
-			fasta=fasta,
-			ref_dir=ref_dir,
-			fastq_1=fastq_1_D6,
-			fastq_2=fastq_2_D6,
-			group=project,
-			sample='LCL6',
-			project=project,
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
-
-		call fastqc.fastqc as fastqc_D6 {
-			input:
-			read1=fastq_1_D6,
-			read2=fastq_2_D6,
-			project=project,
-			sample="LCL6",
-			docker=FASTQCdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size
-		}
-
-		call fastqscreen.fastq_screen as fastqscreen_D6 {
-			input:
-			read1=fastq_1_D6,
-			read2=fastq_2_D6,
-			project=project,
-			sample="LCL6",
-			screen_ref_dir=screen_ref_dir,
-			fastq_screen_conf=fastq_screen_conf,
-			docker=FASTQSCREENdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size
-		}
+		# call mapping.mapping as mapping_D6 {
+		# 	input: 
+		# 	pl=pl,
+		# 	fasta=fasta,
+		# 	ref_dir=ref_dir,
+		# 	fastq_1=fastq_1_D6,
+		# 	fastq_2=fastq_2_D6,
+		# 	group=project,
+		# 	sample='LCL6',
+		# 	project=project,
+		# 	docker=REPLACE_SENTIEON_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
 
-		call Dedup.Dedup as Dedup_D6 {
-			input:
-			sorted_bam=mapping_D6.sorted_bam,
-			sorted_bam_index=mapping_D6.sorted_bam_index,
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
+		# call fastqc.fastqc as fastqc_D6 {
+		# 	input:
+		# 	read1=fastq_1_D6,
+		# 	read2=fastq_2_D6,
+		# 	project=project,
+		# 	sample="LCL6",
+		# 	docker=FASTQCdocker,
+		# 	cluster_config=BIGcluster_config,
+		# 	disk_size=disk_size
+		# }
 
-		call qualimap.qualimap as qualimap_D6 {
-			input:
-			bam=Dedup_D6.Dedup_bam,
-			bai=Dedup_D6.Dedup_bam_index,
-			docker=QUALIMAPdocker,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}		
+		# call fastqscreen.fastq_screen as fastqscreen_D6 {
+		# 	input:
+		# 	read1=fastq_1_D6,
+		# 	read2=fastq_2_D6,
+		# 	project=project,
+		# 	sample="LCL6",
+		# 	screen_ref_dir=screen_ref_dir,
+		# 	fastq_screen_conf=fastq_screen_conf,
+		# 	docker=FASTQSCREENdocker,
+		# 	cluster_config=BIGcluster_config,
+		# 	disk_size=disk_size
+		# }
 
-		call deduped_Metrics.deduped_Metrics as deduped_Metrics_D6 {
-			input:
-			fasta=fasta,
-			ref_dir=ref_dir,
-			Dedup_bam=Dedup_D6.Dedup_bam,
-			Dedup_bam_index=Dedup_D6.Dedup_bam_index,
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
+		# call Dedup.Dedup as Dedup_D6 {
+		# 	input:
+		# 	sorted_bam=mapping_D6.sorted_bam,
+		# 	sorted_bam_index=mapping_D6.sorted_bam_index,
+		# 	docker=REPLACE_SENTIEON_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
 
-		call sentieon.sentieon as sentieon_D6 {
-			input:
-			quality_yield=deduped_Metrics_D6.deduped_QualityYield,
-			wgs_metrics_algo=deduped_Metrics_D6.deduped_wgsmetrics,
-			aln_metrics=deduped_Metrics_D6.dedeuped_aln_metrics,
-			is_metrics=deduped_Metrics_D6.deduped_is_metrics,
-			cluster_config=SMALLcluster_config,
-			disk_size=disk_size		
-		}
+		# call qualimap.qualimap as qualimap_D6 {
+		# 	input:
+		# 	bam=Dedup_D6.Dedup_bam,
+		# 	bai=Dedup_D6.Dedup_bam_index,
+		# 	docker=QUALIMAPdocker,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }		
 
-		# call Realigner.Realigner as Realigner_D6 {
+		# call deduped_Metrics.deduped_Metrics as deduped_Metrics_D6 {
 		# 	input:
-		# 	SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 		# 	fasta=fasta,
 		# 	ref_dir=ref_dir,
 		# 	Dedup_bam=Dedup_D6.Dedup_bam,
 		# 	Dedup_bam_index=Dedup_D6.Dedup_bam_index,
+		# 	docker=REPLACE_SENTIEON_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
+
+		# call sentieon.sentieon as sentieon_D6 {
+		# 	input:
+		# 	quality_yield=deduped_Metrics_D6.deduped_QualityYield,
+		# 	wgs_metrics_algo=deduped_Metrics_D6.deduped_wgsmetrics,
+		# 	aln_metrics=deduped_Metrics_D6.dedeuped_aln_metrics,
+		# 	is_metrics=deduped_Metrics_D6.deduped_is_metrics,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size		
+		# }
+
+		# # call Realigner.Realigner as Realigner_D6 {
+		# # 	input:
+		# # 	SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		# # 	fasta=fasta,
+		# # 	ref_dir=ref_dir,
+		# # 	Dedup_bam=Dedup_D6.Dedup_bam,
+		# # 	Dedup_bam_index=Dedup_D6.Dedup_bam_index,
+		# # 	db_mills=db_mills,
+		# # 	dbmills_dir=dbmills_dir,
+		# # 	docker=SENTIEONdocker,
+		# # 	disk_size=disk_size,
+		# # 	cluster_config=BIGcluster_config
+		# # }
+
+		# call BQSR.BQSR as BQSR_D6 {
+		# 	input:
+		# 	fasta=fasta,
+		# 	ref_dir=ref_dir,
+		# 	realigned_bam=Dedup_D6.Dedup_bam,
+		# 	realigned_bam_index=Dedup_D6.Dedup_bam_index,
 		# 	db_mills=db_mills,
 		# 	dbmills_dir=dbmills_dir,
-		# 	docker=SENTIEONdocker,
+		# 	dbsnp=dbsnp,
+		# 	dbsnp_dir=dbsnp_dir,
+		# 	docker=REPLACE_SENTIEON_DOCKER,
 		# 	disk_size=disk_size,
 		# 	cluster_config=BIGcluster_config
 		# }
 
-		call BQSR.BQSR as BQSR_D6 {
-			input:
-			fasta=fasta,
-			ref_dir=ref_dir,
-			realigned_bam=Dedup_D6.Dedup_bam,
-			realigned_bam_index=Dedup_D6.Dedup_bam_index,
-			db_mills=db_mills,
-			dbmills_dir=dbmills_dir,
-			dbsnp=dbsnp,
-			dbsnp_dir=dbsnp_dir,
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
-
-		call Haplotyper.Haplotyper as Haplotyper_D6 {
-			input:
-			fasta=fasta,
-			ref_dir=ref_dir,
-			recaled_bam=BQSR_D6.recaled_bam,
-			recaled_bam_index=BQSR_D6.recaled_bam_index,
-			docker=DEEPVARIANT_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
+		# call Haplotyper.Haplotyper as Haplotyper_D6 {
+		# 	input:
+		# 	fasta=fasta,
+		# 	ref_dir=ref_dir,
+		# 	recaled_bam=BQSR_D6.recaled_bam,
+		# 	recaled_bam_index=BQSR_D6.recaled_bam_index,
+		# 	docker=DEEPVARIANT_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
 
-		call filter_vcf.filter_vcf as filter_vcf_D6 {
-			input:
-			vcf=Haplotyper_D6.vcf,
-			docker=BEDTOOLSdocker,
-			cluster_config=SMALLcluster_config,
-			disk_size=disk_size			
-		}
+		# call filter_vcf.filter_vcf as filter_vcf_D6 {
+		# 	input:
+		# 	vcf=Haplotyper_D6.vcf,
+		# 	docker=BEDTOOLSdocker,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size			
+		# }
 
-		call benchmark.benchmark as benchmark_D6 {
-			input:
-			filtered_vcf=filter_vcf_D6.filtered_vcf,
-			benchmarking_dir=benchmarking_dir,
-			ref_dir=ref_dir,
-			fasta=fasta,
-			docker=BENCHMARKdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size
-		}
+		# call benchmark.benchmark as benchmark_D6 {
+		# 	input:
+		# 	filtered_vcf=filter_vcf_D6.filtered_vcf,
+		# 	benchmarking_dir=benchmarking_dir,
+		# 	ref_dir=ref_dir,
+		# 	fasta=fasta,
+		# 	docker=BENCHMARKdocker,
+		# 	cluster_config=BIGcluster_config,
+		# 	disk_size=disk_size
+		# }
 	
-		call mapping.mapping as mapping_F7 {
-			input: 
-			pl=pl,
-			fasta=fasta,
-			ref_dir=ref_dir,
-			fastq_1=fastq_1_F7,
-			fastq_2=fastq_2_F7,
-			group=project,
-			sample='LCL7',
-			project=project,
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
-
-		call fastqc.fastqc as fastqc_F7 {
-			input:
-			read1=fastq_1_F7,
-			read2=fastq_2_F7,
-			project=project,
-			sample="LCL7",
-			docker=FASTQCdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size
-		}
-
-		call fastqscreen.fastq_screen as fastqscreen_F7 {
-			input:
-			read1=fastq_1_F7,
-			read2=fastq_2_F7,
-			project=project,
-			sample="LCL7",
-			screen_ref_dir=screen_ref_dir,
-			fastq_screen_conf=fastq_screen_conf,
-			docker=FASTQSCREENdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size
-		}
+		# call mapping.mapping as mapping_F7 {
+		# 	input: 
+		# 	pl=pl,
+		# 	fasta=fasta,
+		# 	ref_dir=ref_dir,
+		# 	fastq_1=fastq_1_F7,
+		# 	fastq_2=fastq_2_F7,
+		# 	group=project,
+		# 	sample='LCL7',
+		# 	project=project,
+		# 	docker=REPLACE_SENTIEON_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
 
-		call Dedup.Dedup as Dedup_F7 {
-			input:
-			sorted_bam=mapping_F7.sorted_bam,
-			sorted_bam_index=mapping_F7.sorted_bam_index,
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
+		# call fastqc.fastqc as fastqc_F7 {
+		# 	input:
+		# 	read1=fastq_1_F7,
+		# 	read2=fastq_2_F7,
+		# 	project=project,
+		# 	sample="LCL7",
+		# 	docker=FASTQCdocker,
+		# 	cluster_config=BIGcluster_config,
+		# 	disk_size=disk_size
+		# }
 
-		call qualimap.qualimap as qualimap_F7 {
-			input:
-			bam=Dedup_F7.Dedup_bam,
-			bai=Dedup_F7.Dedup_bam_index,
-			docker=QUALIMAPdocker,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}		
+		# call fastqscreen.fastq_screen as fastqscreen_F7 {
+		# 	input:
+		# 	read1=fastq_1_F7,
+		# 	read2=fastq_2_F7,
+		# 	project=project,
+		# 	sample="LCL7",
+		# 	screen_ref_dir=screen_ref_dir,
+		# 	fastq_screen_conf=fastq_screen_conf,
+		# 	docker=FASTQSCREENdocker,
+		# 	cluster_config=BIGcluster_config,
+		# 	disk_size=disk_size
+		# }
 
-		call deduped_Metrics.deduped_Metrics as deduped_Metrics_F7 {
-			input:
-			fasta=fasta,
-			ref_dir=ref_dir,
-			Dedup_bam=Dedup_F7.Dedup_bam,
-			Dedup_bam_index=Dedup_F7.Dedup_bam_index,
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
+		# call Dedup.Dedup as Dedup_F7 {
+		# 	input:
+		# 	sorted_bam=mapping_F7.sorted_bam,
+		# 	sorted_bam_index=mapping_F7.sorted_bam_index,
+		# 	docker=REPLACE_SENTIEON_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
 
-		call sentieon.sentieon as sentieon_F7 {
-			input:
-			quality_yield=deduped_Metrics_F7.deduped_QualityYield,
-			wgs_metrics_algo=deduped_Metrics_F7.deduped_wgsmetrics,
-			aln_metrics=deduped_Metrics_F7.dedeuped_aln_metrics,
-			is_metrics=deduped_Metrics_F7.deduped_is_metrics,
-			cluster_config=SMALLcluster_config,
-			disk_size=disk_size		
-		}
+		# call qualimap.qualimap as qualimap_F7 {
+		# 	input:
+		# 	bam=Dedup_F7.Dedup_bam,
+		# 	bai=Dedup_F7.Dedup_bam_index,
+		# 	docker=QUALIMAPdocker,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }		
 
-		# call Realigner.Realigner as Realigner_F7 {
+		# call deduped_Metrics.deduped_Metrics as deduped_Metrics_F7 {
 		# 	input:
-		# 	SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 		# 	fasta=fasta,
 		# 	ref_dir=ref_dir,
 		# 	Dedup_bam=Dedup_F7.Dedup_bam,
 		# 	Dedup_bam_index=Dedup_F7.Dedup_bam_index,
+		# 	docker=REPLACE_SENTIEON_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
+
+		# call sentieon.sentieon as sentieon_F7 {
+		# 	input:
+		# 	quality_yield=deduped_Metrics_F7.deduped_QualityYield,
+		# 	wgs_metrics_algo=deduped_Metrics_F7.deduped_wgsmetrics,
+		# 	aln_metrics=deduped_Metrics_F7.dedeuped_aln_metrics,
+		# 	is_metrics=deduped_Metrics_F7.deduped_is_metrics,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size		
+		# }
+
+		# # call Realigner.Realigner as Realigner_F7 {
+		# # 	input:
+		# # 	SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		# # 	fasta=fasta,
+		# # 	ref_dir=ref_dir,
+		# # 	Dedup_bam=Dedup_F7.Dedup_bam,
+		# # 	Dedup_bam_index=Dedup_F7.Dedup_bam_index,
+		# # 	db_mills=db_mills,
+		# # 	dbmills_dir=dbmills_dir,
+		# # 	docker=SENTIEONdocker,
+		# # 	disk_size=disk_size,
+		# # 	cluster_config=BIGcluster_config
+		# # }
+
+		# call BQSR.BQSR as BQSR_F7 {
+		# 	input:
+		# 	fasta=fasta,
+		# 	ref_dir=ref_dir,
+		# 	realigned_bam=Dedup_F7.Dedup_bam,
+		# 	realigned_bam_index=Dedup_F7.Dedup_bam_index,
 		# 	db_mills=db_mills,
 		# 	dbmills_dir=dbmills_dir,
-		# 	docker=SENTIEONdocker,
+		# 	dbsnp=dbsnp,
+		# 	dbsnp_dir=dbsnp_dir,
+		# 	docker=REPLACE_SENTIEON_DOCKER,
 		# 	disk_size=disk_size,
 		# 	cluster_config=BIGcluster_config
 		# }
 
-		call BQSR.BQSR as BQSR_F7 {
-			input:
-			fasta=fasta,
-			ref_dir=ref_dir,
-			realigned_bam=Dedup_F7.Dedup_bam,
-			realigned_bam_index=Dedup_F7.Dedup_bam_index,
-			db_mills=db_mills,
-			dbmills_dir=dbmills_dir,
-			dbsnp=dbsnp,
-			dbsnp_dir=dbsnp_dir,
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
-
-		call Haplotyper.Haplotyper as Haplotyper_F7 {
-			input:
-			fasta=fasta,
-			ref_dir=ref_dir,
-			recaled_bam=BQSR_F7.recaled_bam,
-			recaled_bam_index=BQSR_F7.recaled_bam_index,
-			docker=DEEPVARIANT_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
+		# call Haplotyper.Haplotyper as Haplotyper_F7 {
+		# 	input:
+		# 	fasta=fasta,
+		# 	ref_dir=ref_dir,
+		# 	recaled_bam=BQSR_F7.recaled_bam,
+		# 	recaled_bam_index=BQSR_F7.recaled_bam_index,
+		# 	docker=DEEPVARIANT_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
 
-		call filter_vcf.filter_vcf as filter_vcf_F7 {
-			input:
-			vcf=Haplotyper_F7.vcf,
-			docker=BEDTOOLSdocker,
-			cluster_config=SMALLcluster_config,
-			disk_size=disk_size			
-		}
+		# call filter_vcf.filter_vcf as filter_vcf_F7 {
+		# 	input:
+		# 	vcf=Haplotyper_F7.vcf,
+		# 	docker=BEDTOOLSdocker,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size			
+		# }
 
-		call benchmark.benchmark as benchmark_F7 {
-			input:
-			filtered_vcf=filter_vcf_F7.filtered_vcf,
-			benchmarking_dir=benchmarking_dir,
-			ref_dir=ref_dir,
-			fasta=fasta,
-			docker=BENCHMARKdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size
-		}
+		# call benchmark.benchmark as benchmark_F7 {
+		# 	input:
+		# 	filtered_vcf=filter_vcf_F7.filtered_vcf,
+		# 	benchmarking_dir=benchmarking_dir,
+		# 	ref_dir=ref_dir,
+		# 	fasta=fasta,
+		# 	docker=BENCHMARKdocker,
+		# 	cluster_config=BIGcluster_config,
+		# 	disk_size=disk_size
+		# }
 	
-		call mapping.mapping as mapping_M8 {
-			input: 
-			pl=pl,
-			fasta=fasta,
-			ref_dir=ref_dir,
-			fastq_1=fastq_1_M8,
-			fastq_2=fastq_2_M8,
-			group=project,
-			project=project,
-			sample='LCL8',
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
-
-		call fastqc.fastqc as fastqc_M8 {
-			input:
-			read1=fastq_1_M8,
-			read2=fastq_2_M8,
-			project=project,
-			sample="LCL8",
-			docker=FASTQCdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size
-		}
-
-		call fastqscreen.fastq_screen as fastqscreen_M8 {
-			input:
-			read1=fastq_1_M8,
-			read2=fastq_2_M8,
-			project=project,
-			sample="LCL8",
-			screen_ref_dir=screen_ref_dir,
-			fastq_screen_conf=fastq_screen_conf,
-			docker=FASTQSCREENdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size
-		}
+		# call mapping.mapping as mapping_M8 {
+		# 	input: 
+		# 	pl=pl,
+		# 	fasta=fasta,
+		# 	ref_dir=ref_dir,
+		# 	fastq_1=fastq_1_M8,
+		# 	fastq_2=fastq_2_M8,
+		# 	group=project,
+		# 	project=project,
+		# 	sample='LCL8',
+		# 	docker=REPLACE_SENTIEON_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
 
-		call Dedup.Dedup as Dedup_M8 {
-			input:
-			sorted_bam=mapping_M8.sorted_bam,
-			sorted_bam_index=mapping_M8.sorted_bam_index,
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
+		# call fastqc.fastqc as fastqc_M8 {
+		# 	input:
+		# 	read1=fastq_1_M8,
+		# 	read2=fastq_2_M8,
+		# 	project=project,
+		# 	sample="LCL8",
+		# 	docker=FASTQCdocker,
+		# 	cluster_config=BIGcluster_config,
+		# 	disk_size=disk_size
+		# }
 
-		call qualimap.qualimap as qualimap_M8 {
-			input:
-			bam=Dedup_M8.Dedup_bam,
-			bai=Dedup_M8.Dedup_bam_index,
-			docker=QUALIMAPdocker,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}		
+		# call fastqscreen.fastq_screen as fastqscreen_M8 {
+		# 	input:
+		# 	read1=fastq_1_M8,
+		# 	read2=fastq_2_M8,
+		# 	project=project,
+		# 	sample="LCL8",
+		# 	screen_ref_dir=screen_ref_dir,
+		# 	fastq_screen_conf=fastq_screen_conf,
+		# 	docker=FASTQSCREENdocker,
+		# 	cluster_config=BIGcluster_config,
+		# 	disk_size=disk_size
+		# }
 
-		call deduped_Metrics.deduped_Metrics as deduped_Metrics_M8 {
-			input:
-			fasta=fasta,
-			ref_dir=ref_dir,
-			Dedup_bam=Dedup_M8.Dedup_bam,
-			Dedup_bam_index=Dedup_M8.Dedup_bam_index,
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
+		# call Dedup.Dedup as Dedup_M8 {
+		# 	input:
+		# 	sorted_bam=mapping_M8.sorted_bam,
+		# 	sorted_bam_index=mapping_M8.sorted_bam_index,
+		# 	docker=REPLACE_SENTIEON_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
 
-		call sentieon.sentieon as sentieon_M8 {
-			input:
-			quality_yield=deduped_Metrics_M8.deduped_QualityYield,
-			wgs_metrics_algo=deduped_Metrics_M8.deduped_wgsmetrics,
-			aln_metrics=deduped_Metrics_M8.dedeuped_aln_metrics,
-			is_metrics=deduped_Metrics_M8.deduped_is_metrics,
-			cluster_config=SMALLcluster_config,
-			disk_size=disk_size		
-		}
+		# call qualimap.qualimap as qualimap_M8 {
+		# 	input:
+		# 	bam=Dedup_M8.Dedup_bam,
+		# 	bai=Dedup_M8.Dedup_bam_index,
+		# 	docker=QUALIMAPdocker,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }		
 
-		# call Realigner.Realigner as Realigner_M8 {
+		# call deduped_Metrics.deduped_Metrics as deduped_Metrics_M8 {
 		# 	input:
-		# 	SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 		# 	fasta=fasta,
 		# 	ref_dir=ref_dir,
 		# 	Dedup_bam=Dedup_M8.Dedup_bam,
 		# 	Dedup_bam_index=Dedup_M8.Dedup_bam_index,
+		# 	docker=REPLACE_SENTIEON_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
+
+		# call sentieon.sentieon as sentieon_M8 {
+		# 	input:
+		# 	quality_yield=deduped_Metrics_M8.deduped_QualityYield,
+		# 	wgs_metrics_algo=deduped_Metrics_M8.deduped_wgsmetrics,
+		# 	aln_metrics=deduped_Metrics_M8.dedeuped_aln_metrics,
+		# 	is_metrics=deduped_Metrics_M8.deduped_is_metrics,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size		
+		# }
+
+		# # call Realigner.Realigner as Realigner_M8 {
+		# # 	input:
+		# # 	SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		# # 	fasta=fasta,
+		# # 	ref_dir=ref_dir,
+		# # 	Dedup_bam=Dedup_M8.Dedup_bam,
+		# # 	Dedup_bam_index=Dedup_M8.Dedup_bam_index,
+		# # 	db_mills=db_mills,
+		# # 	dbmills_dir=dbmills_dir,
+		# # 	docker=SENTIEONdocker,
+		# # 	disk_size=disk_size,
+		# # 	cluster_config=BIGcluster_config
+		# # }
+
+		# call BQSR.BQSR as BQSR_M8 {
+		# 	input:
+		# 	fasta=fasta,
+		# 	ref_dir=ref_dir,
+		# 	realigned_bam=Dedup_M8.Dedup_bam,
+		# 	realigned_bam_index=Dedup_M8.Dedup_bam_index,
 		# 	db_mills=db_mills,
 		# 	dbmills_dir=dbmills_dir,
-		# 	docker=SENTIEONdocker,
+		# 	dbsnp=dbsnp,
+		# 	dbsnp_dir=dbsnp_dir,
+		# 	docker=REPLACE_SENTIEON_DOCKER,
 		# 	disk_size=disk_size,
 		# 	cluster_config=BIGcluster_config
 		# }
 
-		call BQSR.BQSR as BQSR_M8 {
-			input:
-			fasta=fasta,
-			ref_dir=ref_dir,
-			realigned_bam=Dedup_M8.Dedup_bam,
-			realigned_bam_index=Dedup_M8.Dedup_bam_index,
-			db_mills=db_mills,
-			dbmills_dir=dbmills_dir,
-			dbsnp=dbsnp,
-			dbsnp_dir=dbsnp_dir,
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
-
-		call Haplotyper.Haplotyper as Haplotyper_M8 {
-			input:
-			fasta=fasta,
-			ref_dir=ref_dir,
-			recaled_bam=BQSR_M8.recaled_bam,
-			recaled_bam_index=BQSR_M8.recaled_bam_index,
-			docker=DEEPVARIANT_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
+		# call Haplotyper.Haplotyper as Haplotyper_M8 {
+		# 	input:
+		# 	fasta=fasta,
+		# 	ref_dir=ref_dir,
+		# 	recaled_bam=BQSR_M8.recaled_bam,
+		# 	recaled_bam_index=BQSR_M8.recaled_bam_index,
+		# 	docker=DEEPVARIANT_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
 
-		call filter_vcf.filter_vcf as filter_vcf_M8 {
-			input:
-			vcf=Haplotyper_M8.vcf,
-			docker=BEDTOOLSdocker,
-			cluster_config=SMALLcluster_config,
-			disk_size=disk_size			
-		}
+		# call filter_vcf.filter_vcf as filter_vcf_M8 {
+		# 	input:
+		# 	vcf=Haplotyper_M8.vcf,
+		# 	docker=BEDTOOLSdocker,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size			
+		# }
 
-		call benchmark.benchmark as benchmark_M8 {
-			input:
-			filtered_vcf=filter_vcf_M8.filtered_vcf,
-			benchmarking_dir=benchmarking_dir,
-			ref_dir=ref_dir,
-			fasta=fasta,
-			docker=BENCHMARKdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size
-		}
+		# call benchmark.benchmark as benchmark_M8 {
+		# 	input:
+		# 	filtered_vcf=filter_vcf_M8.filtered_vcf,
+		# 	benchmarking_dir=benchmarking_dir,
+		# 	ref_dir=ref_dir,
+		# 	fasta=fasta,
+		# 	docker=BENCHMARKdocker,
+		# 	cluster_config=BIGcluster_config,
+		# 	disk_size=disk_size
+		# }
 	
 
-	    Array[File] fastqc_read1_zip = [fastqc_D5.read1_zip, fastqc_D6.read1_zip, fastqc_F7.read1_zip, fastqc_M8.read1_zip]
+	    # Array[File] fastqc_read1_zip = [fastqc_D5.read1_zip, fastqc_D6.read1_zip, fastqc_F7.read1_zip, fastqc_M8.read1_zip]
 
-	    Array[File] fastqc_read2_zip = [fastqc_D5.read2_zip, fastqc_D6.read2_zip, fastqc_F7.read2_zip, fastqc_M8.read2_zip]
+	    # Array[File] fastqc_read2_zip = [fastqc_D5.read2_zip, fastqc_D6.read2_zip, fastqc_F7.read2_zip, fastqc_M8.read2_zip]
 
-	    Array[File] fastqscreen_txt1 = [fastqscreen_D5.txt1, fastqscreen_D6.txt1, fastqscreen_F7.txt1, fastqscreen_M8.txt1]
+	    # Array[File] fastqscreen_txt1 = [fastqscreen_D5.txt1, fastqscreen_D6.txt1, fastqscreen_F7.txt1, fastqscreen_M8.txt1]
 
-	    Array[File] fastqscreen_txt2 = [fastqscreen_D5.txt2, fastqscreen_D6.txt2, fastqscreen_F7.txt2, fastqscreen_M8.txt2]
+	    # Array[File] fastqscreen_txt2 = [fastqscreen_D5.txt2, fastqscreen_D6.txt2, fastqscreen_F7.txt2, fastqscreen_M8.txt2]
 
-	    Array[File] benchmark_summary = [benchmark_D5.summary, benchmark_D6.summary, benchmark_F7.summary, benchmark_M8.summary]
+	    # Array[File] benchmark_summary = [benchmark_D5.summary, benchmark_D6.summary, benchmark_F7.summary, benchmark_M8.summary]
 
-		call multiqc.multiqc as multiqc_big {
-			input:
-			read1_zip=fastqc_read1_zip,
-			read2_zip=fastqc_read2_zip,
-			txt1=fastqscreen_txt1,
-			txt2=fastqscreen_txt2,
-			summary=benchmark_summary,
-			docker=MULTIQCdocker,
-			cluster_config=SMALLcluster_config,
-			disk_size=disk_size
-		}
+		# call multiqc.multiqc as multiqc_big {
+		# 	input:
+		# 	read1_zip=fastqc_read1_zip,
+		# 	read2_zip=fastqc_read2_zip,
+		# 	txt1=fastqscreen_txt1,
+		# 	txt2=fastqscreen_txt2,
+		# 	summary=benchmark_summary,
+		# 	docker=MULTIQCdocker,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size
+		# }
 
 
-		Array[File] sentieon_quality_yield_header = [sentieon_D5.quality_yield_header, sentieon_D6.quality_yield_header, sentieon_F7.quality_yield_header, sentieon_M8.quality_yield_header]
+		# Array[File] sentieon_quality_yield_header = [sentieon_D5.quality_yield_header, sentieon_D6.quality_yield_header, sentieon_F7.quality_yield_header, sentieon_M8.quality_yield_header]
 
-		Array[File] sentieon_wgs_metrics_algo_header = [sentieon_D5.wgs_metrics_algo_header, sentieon_D6.wgs_metrics_algo_header, sentieon_F7.wgs_metrics_algo_header, sentieon_M8.wgs_metrics_algo_header]
+		# Array[File] sentieon_wgs_metrics_algo_header = [sentieon_D5.wgs_metrics_algo_header, sentieon_D6.wgs_metrics_algo_header, sentieon_F7.wgs_metrics_algo_header, sentieon_M8.wgs_metrics_algo_header]
 
-		Array[File] sentieon_aln_metrics_header = [sentieon_D5.aln_metrics_header, sentieon_D6.aln_metrics_header, sentieon_F7.aln_metrics_header, sentieon_M8.aln_metrics_header]
+		# Array[File] sentieon_aln_metrics_header = [sentieon_D5.aln_metrics_header, sentieon_D6.aln_metrics_header, sentieon_F7.aln_metrics_header, sentieon_M8.aln_metrics_header]
 
-		Array[File] sentieon_is_metrics_header = [sentieon_D5.is_metrics_header, sentieon_D6.is_metrics_header, sentieon_F7.is_metrics_header, sentieon_M8.is_metrics_header]
+		# Array[File] sentieon_is_metrics_header = [sentieon_D5.is_metrics_header, sentieon_D6.is_metrics_header, sentieon_F7.is_metrics_header, sentieon_M8.is_metrics_header]
 
-		Array[File] sentieon_quality_yield_data = [sentieon_D5.quality_yield_data, sentieon_D6.quality_yield_data, sentieon_F7.quality_yield_data, sentieon_M8.quality_yield_data]
+		# Array[File] sentieon_quality_yield_data = [sentieon_D5.quality_yield_data, sentieon_D6.quality_yield_data, sentieon_F7.quality_yield_data, sentieon_M8.quality_yield_data]
 
-		Array[File] sentieon_wgs_metrics_algo_data = [sentieon_D5.wgs_metrics_algo_data, sentieon_D6.wgs_metrics_algo_data, sentieon_F7.wgs_metrics_algo_data, sentieon_M8.wgs_metrics_algo_data]
+		# Array[File] sentieon_wgs_metrics_algo_data = [sentieon_D5.wgs_metrics_algo_data, sentieon_D6.wgs_metrics_algo_data, sentieon_F7.wgs_metrics_algo_data, sentieon_M8.wgs_metrics_algo_data]
 
-		Array[File] sentieon_aln_metrics_data = [sentieon_D5.aln_metrics_data, sentieon_D6.aln_metrics_data, sentieon_F7.aln_metrics_data, sentieon_M8.aln_metrics_data]
+		# Array[File] sentieon_aln_metrics_data = [sentieon_D5.aln_metrics_data, sentieon_D6.aln_metrics_data, sentieon_F7.aln_metrics_data, sentieon_M8.aln_metrics_data]
 
-		Array[File] sentieon_is_metrics_data = [sentieon_D5.is_metrics_data, sentieon_D6.is_metrics_data, sentieon_F7.is_metrics_data, sentieon_M8.is_metrics_data]
+		# Array[File] sentieon_is_metrics_data = [sentieon_D5.is_metrics_data, sentieon_D6.is_metrics_data, sentieon_F7.is_metrics_data, sentieon_M8.is_metrics_data]
 
-		call merge_sentieon_metrics.merge_sentieon_metrics as merge_sentieon_metrics {
-			input:
-			quality_yield_header=sentieon_quality_yield_header,
-			wgs_metrics_algo_header=sentieon_wgs_metrics_algo_header,
-			aln_metrics_header=sentieon_aln_metrics_header,
-			is_metrics_header=sentieon_is_metrics_header,
-			quality_yield_data=sentieon_quality_yield_data,
-			wgs_metrics_algo_data=sentieon_wgs_metrics_algo_data,
-			aln_metrics_data=sentieon_aln_metrics_data,
-			is_metrics_data=sentieon_is_metrics_data,
-			project=project,
-			docker=MULTIQCdocker,
-			cluster_config=SMALLcluster_config,
-			disk_size=disk_size	
-		}
+		# call merge_sentieon_metrics.merge_sentieon_metrics as merge_sentieon_metrics {
+		# 	input:
+		# 	quality_yield_header=sentieon_quality_yield_header,
+		# 	wgs_metrics_algo_header=sentieon_wgs_metrics_algo_header,
+		# 	aln_metrics_header=sentieon_aln_metrics_header,
+		# 	is_metrics_header=sentieon_is_metrics_header,
+		# 	quality_yield_data=sentieon_quality_yield_data,
+		# 	wgs_metrics_algo_data=sentieon_wgs_metrics_algo_data,
+		# 	aln_metrics_data=sentieon_aln_metrics_data,
+		# 	is_metrics_data=sentieon_is_metrics_data,
+		# 	project=project,
+		# 	docker=MULTIQCdocker,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size	
+		# }
 
-		call extract_tables.extract_tables as extract_tables {
-			input:
-			quality_yield_summary=merge_sentieon_metrics.quality_yield_summary,
-			wgs_metrics_summary=merge_sentieon_metrics.wgs_metrics_summary,
-			aln_metrics_summary=merge_sentieon_metrics.aln_metrics_summary,
-			is_metrics_summary=merge_sentieon_metrics.is_metrics_summary,
-			fastqc=multiqc_big.fastqc,
-			fastqscreen=multiqc_big.fastqscreen,
-			hap=multiqc_big.hap,
-			project=project,
-			docker=DIYdocker,
-			cluster_config=SMALLcluster_config,
-			disk_size=disk_size
-		}
+		# call extract_tables.extract_tables as extract_tables {
+		# 	input:
+		# 	quality_yield_summary=merge_sentieon_metrics.quality_yield_summary,
+		# 	wgs_metrics_summary=merge_sentieon_metrics.wgs_metrics_summary,
+		# 	aln_metrics_summary=merge_sentieon_metrics.aln_metrics_summary,
+		# 	is_metrics_summary=merge_sentieon_metrics.is_metrics_summary,
+		# 	fastqc=multiqc_big.fastqc,
+		# 	fastqscreen=multiqc_big.fastqscreen,
+		# 	hap=multiqc_big.hap,
+		# 	project=project,
+		# 	docker=DIYdocker,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size
+		# }
 
-		call merge_family.merge_family as merge_family {
-			input:
-			D5_vcf=benchmark_D5.rtg_vcf,
-			D6_vcf=benchmark_D6.rtg_vcf,
-			F7_vcf=benchmark_F7.rtg_vcf,
-			M8_vcf=benchmark_M8.rtg_vcf,
-			D5_vcf_tbi=benchmark_D5.rtg_vcf_index,
-			D6_vcf_tbi=benchmark_D6.rtg_vcf_index,
-			F7_vcf_tbi=benchmark_F7.rtg_vcf_index,
-			M8_vcf_tbi=benchmark_M8.rtg_vcf_index,
-			project=project,
-			docker=BENCHMARKdocker,
-			cluster_config=SMALLcluster_config,
-			disk_size=disk_size,
-		}
+		# call merge_family.merge_family as merge_family {
+		# 	input:
+		# 	D5_vcf=benchmark_D5.rtg_vcf,
+		# 	D6_vcf=benchmark_D6.rtg_vcf,
+		# 	F7_vcf=benchmark_F7.rtg_vcf,
+		# 	M8_vcf=benchmark_M8.rtg_vcf,
+		# 	D5_vcf_tbi=benchmark_D5.rtg_vcf_index,
+		# 	D6_vcf_tbi=benchmark_D6.rtg_vcf_index,
+		# 	F7_vcf_tbi=benchmark_F7.rtg_vcf_index,
+		# 	M8_vcf_tbi=benchmark_M8.rtg_vcf_index,
+		# 	project=project,
+		# 	docker=BENCHMARKdocker,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size,
+		# }
 
-		call mendelian.mendelian as mendelian {
-			input:
-			family_vcf=merge_family.family_vcf,
-			ref_dir=ref_dir,
-			fasta=fasta,
-			docker=MENDELIANdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size		
-		}
+		# call mendelian.mendelian as mendelian {
+		# 	input:
+		# 	family_vcf=merge_family.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=merge_family.family_vcf,
-			docker=DIYdocker,
-			cluster_config=SMALLcluster_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=merge_family.family_vcf,
+		# 	docker=DIYdocker,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size
+		# }
 	}
 
 	# if start with vcf