test13

workflow.wdl

@@ -86,29 +86,29 @@ workflow {{ project_name }} {
 			cluster_config=BIGcluster_config
 		}
 
-		call fastqc.fastqc as fastqc_D5 {
-			input:
-			read1=fastq_1_D5,
-			read2=fastq_2_D5,
-			project=project,
-			sample="LCL5",
-			docker=FASTQCdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size
-		}
+		# call fastqc.fastqc as fastqc_D5 {
+		# 	input:
+		# 	read1=fastq_1_D5,
+		# 	read2=fastq_2_D5,
+		# 	project=project,
+		# 	sample="LCL5",
+		# 	docker=FASTQCdocker,
+		# 	cluster_config=BIGcluster_config,
+		# 	disk_size=disk_size
+		# }
 
-		call fastqscreen.fastq_screen as fastqscreen_D5 {
-			input:
-			read1=fastq_1_D5,
-			read2=fastq_2_D5,
-			project=project,
-			sample="LCL5",
-			screen_ref_dir=screen_ref_dir,
-			fastq_screen_conf=fastq_screen_conf,
-			docker=FASTQSCREENdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size
-		}
+		# call fastqscreen.fastq_screen as fastqscreen_D5 {
+		# 	input:
+		# 	read1=fastq_1_D5,
+		# 	read2=fastq_2_D5,
+		# 	project=project,
+		# 	sample="LCL5",
+		# 	screen_ref_dir=screen_ref_dir,
+		# 	fastq_screen_conf=fastq_screen_conf,
+		# 	docker=FASTQSCREENdocker,
+		# 	cluster_config=BIGcluster_config,
+		# 	disk_size=disk_size
+		# }
 
 		call Dedup.Dedup as Dedup_D5 {
 			input:
@@ -119,35 +119,35 @@ workflow {{ project_name }} {
 			cluster_config=BIGcluster_config
 		}
 
-		call qualimap.qualimap as qualimap_D5 {
-			input:
-			bam=Dedup_D5.Dedup_bam,
-			bai=Dedup_D5.Dedup_bam_index,
-			docker=QUALIMAPdocker,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}		
+		# call qualimap.qualimap as qualimap_D5 {
+		# 	input:
+		# 	bam=Dedup_D5.Dedup_bam,
+		# 	bai=Dedup_D5.Dedup_bam_index,
+		# 	docker=QUALIMAPdocker,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }		
 
-		call deduped_Metrics.deduped_Metrics as deduped_Metrics_D5 {
-			input:
-			fasta=fasta,
-			ref_dir=ref_dir,
-			Dedup_bam=Dedup_D5.Dedup_bam,
-			Dedup_bam_index=Dedup_D5.Dedup_bam_index,
-			docker=REPLACE_SENTIEON_DOCKER,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
+		# call deduped_Metrics.deduped_Metrics as deduped_Metrics_D5 {
+		# 	input:
+		# 	fasta=fasta,
+		# 	ref_dir=ref_dir,
+		# 	Dedup_bam=Dedup_D5.Dedup_bam,
+		# 	Dedup_bam_index=Dedup_D5.Dedup_bam_index,
+		# 	docker=REPLACE_SENTIEON_DOCKER,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
 
-		call sentieon.sentieon as sentieon_D5 {
-			input:
-			quality_yield=deduped_Metrics_D5.deduped_QualityYield,
-			wgs_metrics_algo=deduped_Metrics_D5.deduped_wgsmetrics,
-			aln_metrics=deduped_Metrics_D5.dedeuped_aln_metrics,
-			is_metrics=deduped_Metrics_D5.deduped_is_metrics,
-			cluster_config=SMALLcluster_config,
-			disk_size=disk_size		
-		}
+		# call sentieon.sentieon as sentieon_D5 {
+		# 	input:
+		# 	quality_yield=deduped_Metrics_D5.deduped_QualityYield,
+		# 	wgs_metrics_algo=deduped_Metrics_D5.deduped_wgsmetrics,
+		# 	aln_metrics=deduped_Metrics_D5.dedeuped_aln_metrics,
+		# 	is_metrics=deduped_Metrics_D5.deduped_is_metrics,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size		
+		# }
 
 		### Bam realignment doesn't support in GATK 4
 		# call Realigner.Realigner as Realigner_D5 {