更新 'tasks/battenberg.wdl'

tasks/battenberg.wdl

@@ -14,10 +14,17 @@ task battenberg {
         set -e
         cp ${normal_bam} ./${normal_id}.bam
         cp ${tumor_bam} ./${sample_id}.bam
-        samtools view -h ./${normal_id}.bam |sed 's/chr//g'|samtools view  -bS -o ./${normal_id}.sorted.deduped.nochr.bam
-        samtools view -h ./${sample_id}.bam |sed 's/chr//g'|samtools view  -bS -o ./${sample_id}.sorted.deduped.nochr.bam
-      
-     
+
+        samtools view -@ 28 -o ${normal_id}.sorted.deduped.sam ./${normal_id}.bam
+        samtools view -@ 28 -o ${sample_id}.sorted.deduped.sam ./${sample_id}.bam
+
+        sed -i 's/chr//g' ${normal_id}.sorted.deduped.sam
+        sed -i 's/chr//g' ${sample_id}.sorted.deduped.sam
+
+        samtools sort -@ 28 -o ${normal_id}.sorted.deduped.nochr.bam ${normal_id}.sorted.deduped.sam
+        samtools sort -@ 28 -o ${sample_id}.sorted.deduped.nochr.bam ${sample_id}.sorted.deduped.sam
+   
+
 
     >>>