update: depth.wdl

inputs

@@ -1,7 +1,9 @@
 {
   "{{ project_name }}.sample_id": "{{ sample_id }}",
-  "{{ project_name }}.bam": "{{ bam }}",
-  "{{ project_name }}.bam_idx": "{{ bam_idx }}",
+  "{{ project_name }}.raw_bam": "{{ raw_bam }}",
+  "{{ project_name }}.raw_bam_idx": "{{ raw_bam_idx }}",
+  "{{ project_name }}.deduped_bam": "{{ deduped_bam }}",
+  "{{ project_name }}.deduped_bam_idx": "{{ deduped_bam_idx }}",
   "{{ project_name }}.regions": "{{ regions }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.docker": "{{ docker }}",

tasks/depth.wdl

@@ -1,6 +1,8 @@
 task depth {
-	File bam
-	File bam_idx
+	File raw_bam
+	File raw_bam_idx
+	File deduped_bam
+	File deduped_bam_idx
 	String sample_id
 	File regions
 	String docker
@@ -8,7 +10,11 @@ task depth {
 	String disk_size
 	
 	command <<<
-		/opt/conda/bin/samtools depth -b ${regions} ${bam} > ${sample_id}.depth
+		/opt/conda/bin/samtools depth -b ${regions} ${raw_bam} > ${sample_id}.raw.depth
+		/opt/conda/bin/samtools depth -b ${regions} ${dedup_bam} > ${sample_id}.deduped.depth
+		awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' ${sample_id}.raw.depth | sort > ${sample_id}.raw.sorted.depth
+		awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' ${sample_id}.deduped.depth | sort > ${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 {

workflow.wdl

@@ -1,9 +1,10 @@
 import "./tasks/depth.wdl" as depth
 
-
 workflow {{ project_name }} {
-	File bam
-	File bam_idx
+	File raw_bam
+	File raw_bam_idx
+	File deduped_bam
+	File deduped_bam_idx
 	String sample_id
 	File regions
 	String docker
@@ -12,8 +13,10 @@ workflow {{ project_name }} {
 
 	call depth.depth as depth {
 		input:	
-		bam=bam,
-		bam_idx=bam_idx,
+		raw_bam=raw_bam,
+		raw_bam_idx=raw_bam_idx,
+		deduped_bam=deduped_bam,
+		deduped_bam_idx=deduped_bam_idx,
 		sample_id=sample_id,
 		regions=regions,
 		docker=docker,