update workflow

tasks/deduped_depth.wdl

+task depth {
+	File deduped_bam
+	File deduped_bam_idx
+	String sample_id
+	File regions
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		/opt/conda/bin/samtools depth -aa -b ${regions} ${deduped_bam} > ${sample_id}.deduped.depth
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File deduped_depth = "${sample_id}.deduped.depth"
+	}
+}

tasks/depth.wdl

 task depth {
-	File raw_bam
-	File raw_bam_idx
-	File deduped_bam
-	File deduped_bam_idx
-	String sample_id
-	File regions
-	String docker
-	String cluster_config
-	String disk_size
-	
-	command <<<
-		/opt/conda/bin/samtools depth -aa -b ${regions} ${raw_bam} > ${sample_id}.raw.depth
-		/opt/conda/bin/samtools depth -aa -b ${regions} ${deduped_bam} > ${sample_id}.deduped.depth
-		sort -k1,1V -k2,2n ${sample_id}.raw.depth | awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' > ${sample_id}.raw.sorted.depth
-		sort -k1,1V -k2,2n ${sample_id}.deduped.depth | awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' > ${sample_id}.deduped.sorted.depth
-		join -e NULL -a1 -j 1 -o 1.1,1.2,2.2 ${sample_id}.raw.sorted.depth ${sample_id}.deduped.sorted.depth > ${sample_id}.depth
-	>>>
+    File raw_depth
+    File deduped_depth
+    String sample_id
+    File regions
+    String docker
+    String cluster_config
+    String disk_size
+    
+    command <<<
+        sort -k1,1V -k2,2n ${raw_depth} | awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' > ${sample_id}.raw.sorted.depth
+        sort -k1,1V -k2,2n ${deduped_depth} | awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' > ${sample_id}.deduped.sorted.depth
+        join -e NULL -a1 -j 1 -o 1.1,1.2,2.2 ${sample_id}.raw.sorted.depth ${sample_id}.deduped.sorted.depth > ${sample_id}.depth
+    >>>
 
-	runtime {
-		docker:docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-	output {
-		File bam_depth = "${sample_id}.depth"
-	}
+    runtime {
+        docker:docker
+        cluster: cluster_config
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+    output {
+        File bam_depth = "${sample_id}.depth"
+    }
 }

tasks/raw_depth.wdl

+task depth {
+	File raw_bam
+	File raw_bam_idx
+	String sample_id
+	File regions
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		/opt/conda/bin/samtools depth -aa -b ${regions} ${raw_bam} > ${sample_id}.raw.depth
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File raw_depth = "${sample_id}.raw.depth"
+	}
+}

workflow.wdl

+import "./tasks/raw_depth.wdl" as raw_depth
+import "./tasks/deduped_depth.wdl" as deduped_depth
 import "./tasks/depth.wdl" as depth
 
 workflow {{ project_name }} {
 	String cluster_config
 	String disk_size
 
-	call depth.depth as depth {
+	call raw_depth.raw_depth as raw_depth {
 		input:	
 		raw_bam=raw_bam,
 		raw_bam_idx=raw_bam_idx,
+		sample_id=sample_id,
+		regions=regions,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+
+	call deduped_depth.deduped_depth as deduped_depth {
+		input:
 		deduped_bam=deduped_bam,
 		deduped_bam_idx=deduped_bam_idx,
 		sample_id=sample_id,
 		cluster_config=cluster_config,
 		disk_size=disk_size
 	}
+
+	call depth.depth as depth {
+		input:	
+		raw_depth=raw_depth,
+		deduped_depth=deduped_depth,
+		sample_id=sample_id,
+		regions=regions,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
 }