fix bug: workflow input

tasks/deduped_depth.wdl

@@ -18,6 +18,6 @@ task depth {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File deduped_depth = "${sample_id}.deduped.depth"
+		File bam_deduped_depth = "${sample_id}.deduped.depth"
 	}
 }

tasks/depth.wdl

@@ -1,6 +1,6 @@
 task depth {
-    File raw_depth
-    File deduped_depth
+    File bam_raw_depth
+    File bam_deduped_depth
     String sample_id
     File regions
     String docker
@@ -8,8 +8,8 @@ task depth {
     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
+        sort -k1,1V -k2,2n ${bam_raw_depth} | awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' > ${sample_id}.raw.sorted.depth
+        sort -k1,1V -k2,2n ${bam_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
     >>>
 

tasks/raw_depth.wdl

@@ -18,6 +18,6 @@ task depth {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File raw_depth = "${sample_id}.raw.depth"
+		File bam_raw_depth = "${sample_id}.raw.depth"
 	}
 }

workflow.wdl

@@ -37,8 +37,8 @@ workflow {{ project_name }} {
 
 	call depth.depth as depth {
 		input:	
-		raw_depth=raw_depth.raw_depth,
-		deduped_depth=deduped_depth.deduped_depth,
+		bam_raw_depth=raw_depth.bam_raw_depth,
+		bam_deduped_depth=deduped_depth.bam_deduped_depth,
 		sample_id=sample_id,
 		regions=regions,
 		docker=docker,