dedup

tasks/Dedup.wdl

@@ -0,0 +1,40 @@
+task Dedup {
+
+	String SENTIEON_INSTALL_DIR
+	String sample
+	String type
+	File sorted_bam
+	File sorted_bam_index
+	String docker
+	String cluster_config
+	String disk_size
+
+
+	command <<<
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo LocusCollector --fun score_info ${sample}.${type}_score.txt
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo Dedup --rmdup --score_info ${sample}.${type}_score.txt --metrics ${sample}.${type}_dedup_metrics.txt ${sample}.${type}.sorted.deduped.bam	
+	>>>
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File score = "${sample}.${type}_score.txt"
+		File dedup_metrics = "${sample}.${type}_dedup_metrics.txt"
+		File Dedup_bam = "${sample}.${type}.sorted.deduped.bam"
+		File Dedup_bam_index = "${sample}.${type}.sorted.deduped.bam.bai"
+	}
+}
+
+
+
+
+
+

workflow.wdl

@@ -53,13 +53,36 @@ workflow {{ project_name }} {
 		cluster_config=BIGcluster_config
 	}
 
-	
+	call Dedup.Dedup as tumor_Dedup {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		sorted_bam=tumor_mapping.sorted_bam,
+		sorted_bam_index=tumor_mapping.sorted_bam_index,
+		sample=sample_name,
+		type="tumor"
+		docker=SENTIEONdocker,
+		disk_size=disk_size,
+		cluster_config=BIGcluster_config
+	}
+
+	call Dedup.Dedup as normal_Dedup {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		sorted_bam=normal_mapping.sorted_bam,
+		sorted_bam_index=normal_mapping.sorted_bam_index,
+		sample=sample_name,
+		type="normal"
+		docker=SENTIEONdocker,
+		disk_size=disk_size,
+		cluster_config=BIGcluster_config
+	}
+
 	call delly.delly as delly {
 		input: 
-		tumor_bam=tumor_mapping.sorted_bam,
-		tumor_bam_idx=tumor_mapping.sorted_bam_index,
-		normal_bam=normal_mapping.sorted_bam,
-		normal_bam_idx=normal_mapping.sorted_bam_index,
+		tumor_bam=tumor_Dedup.Dedup_bam,
+		tumor_bam_idx=tumor_Dedup.Dedup_bam_index,
+		normal_bam=normal_Dedup.Dedup_bam,
+		normal_bam_idx=normal_Dedup.Dedup_bam_index,
 		ref_dir=ref_dir,
 		fasta=fasta,
 		sample_name=sample_name,