add indel realignment

tasks/Realigner.wdl

@@ -0,0 +1,40 @@
+task Realigner {
+
+    File ref_dir
+    File dbmills_dir
+
+	String fasta
+
+	File Dedup_bam
+	File Dedup_bam_index
+	String sample = basename(Dedup_bam,".sorted.deduped.bam")
+	String db_mills
+	String docker	
+	String cluster_config
+	String disk_size
+
+
+	command <<<
+	set -o pipefail
+	set -e
+	nt=$(nproc)
+	/usr/local/jdk-1.8.0/bin/java -jar /usr/local/GenomeAnalysisTK.jar -T RealignerTargetCreator -R ${ref_dir}/${fasta} -nt $nt -I ${Dedup_bam} -known ${dbmills_dir}/${db_mills} -o ${sample}.IndelRealigner.intervals
+	/usr/local/jdk-1.8.0/bin/java -jar /usr/local/GenomeAnalysisTK.jar -T IndelRealigner -R ${ref_dir}/${fasta} -I ${Dedup_bam} --targetIntervals ${sample}.IndelRealigner.intervals -o ${sample}.sorted.deduped.realigned.bam
+	/usr/local/samtools-1.17/bin/samtools index -@ $(nproc) -o  ${sample}.sorted.deduped.realigned.bam.bai  ${sample}.sorted.deduped.realigned.bam
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File realigner_bam = "${sample}.sorted.deduped.realigned.bam"
+		File realigner_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"
+
+	}
+}
+
+

workflow.wdl

@@ -5,6 +5,7 @@ import "./tasks/Dedup.wdl" as Dedup
 import "./tasks/qualimap.wdl" as qualimap
 import "./tasks/deduped_Metrics.wdl" as deduped_Metrics
 import "./tasks/sentieon.wdl" as sentieon
+import "./tasks/Realigner.wdl" as Realigner
 import "./tasks/BQSR.wdl" as BQSR
 import "./tasks/Haplotyper.wdl" as Haplotyper
 import "./tasks/benchmark.wdl" as benchmark
@@ -152,27 +153,26 @@ workflow {{ project_name }} {
 			disk_size=disk_size		
 		}
 
-		### Bam realignment doesn't support in GATK 4
-		# call Realigner.Realigner as Realigner_D5 {
-		# 	input:
-		# 	SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		# 	fasta=fasta,
-		# 	ref_dir=ref_dir,
-		# 	Dedup_bam=Dedup_D5.Dedup_bam,
-		# 	Dedup_bam_index=Dedup_D5.Dedup_bam_index,
-		# 	db_mills=db_mills,
-		# 	dbmills_dir=dbmills_dir,
-		# 	docker=SENTIEONdocker,
-		# 	disk_size=disk_size,
-		# 	cluster_config=BIGcluster_config
-		# }
+		## Bam realignment doesn't support in GATK 4
+		call Realigner.Realigner as Realigner_D5 {
+			input:
+			fasta=fasta,
+			ref_dir=ref_dir,
+			Dedup_bam=Dedup_D5.Dedup_bam,
+			Dedup_bam_index=Dedup_D5.Dedup_bam_index,
+			db_mills=db_mills,
+			dbmills_dir=dbmills_dir,
+			docker=REPLACE_SENTIEON_DOCKER,
+			disk_size=disk_size,
+			cluster_config=BIGcluster_config
+		}
 
 		call BQSR.BQSR as BQSR_D5 {
 			input:
 			fasta=fasta,
 			ref_dir=ref_dir,
-			realigned_bam=Dedup_D5.Dedup_bam,
-			realigned_bam_index=Dedup_D5.Dedup_bam_index,
+			realigned_bam=Realigner_D5.realigner_bam,
+			realigned_bam_index=Realigner_D5.realigner_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
@@ -290,26 +290,25 @@ workflow {{ project_name }} {
 			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 Realigner.Realigner as Realigner_D6 {
+			input:
+			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=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,
+			realigned_bam=Realigner_D6.realigner_bam,
+			realigned_bam_index=Realigner_D6.realigner_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
@@ -427,26 +426,25 @@ workflow {{ project_name }} {
 			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 Realigner.Realigner as Realigner_F7 {
+			input:
+			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=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,
+			realigned_bam=Realigner_F7.realigner_bam,
+			realigned_bam_index=Realigner_F7.realigner_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
@@ -564,26 +562,25 @@ workflow {{ project_name }} {
 			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 Realigner.Realigner as Realigner_M8 {
+			input:
+			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=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,
+			realigned_bam=Realigner_M8.realigner_bam,
+			realigned_bam_index=Realigner_M8.realigner_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,