更新 'tasks/battenberg.wdl'

tasks/battenberg.wdl

@@ -14,8 +14,8 @@ task battenberg {
         set -e
         cp ${normal_bam} ./${normal_id}.bam
         cp ${tumor_bam} ./${sample_id}.bam
-        samtools view -h ./${normal_id}.bam |sed 's/chr//g'|samtools view  -bS > ./${normal_id}.sorted.deduped.nochr.bam
-        samtools view -h ./${sample_id}.bam |sed 's/chr//g'|samtools view  -bS > ./${sample_id}.sorted.deduped.nochr.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 index  ./${normal_id}.sorted.deduped.nochr.bam