update: depth.wdl

tasks/depth.wdl

@@ -10,10 +10,10 @@ task depth {
 	String disk_size
 	
 	command <<<
-		/opt/conda/bin/samtools depth -b ${regions} ${raw_bam} > ${sample_id}.raw.depth
-		/opt/conda/bin/samtools depth -b ${regions} ${deduped_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
+		/opt/conda/bin/samtools depth -a -b ${regions} ${raw_bam} > ${sample_id}.raw.depth
+		/opt/conda/bin/samtools depth -a -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
 	>>>