更新 'tasks/battenberg.wdl'

{normal_id}.sorted.deduped.nochr.bam

tasks/battenberg.wdl

@@ -15,6 +15,9 @@ task battenberg {
         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
+
 
     >>>
 
@@ -26,8 +29,8 @@ task battenberg {
     }
 
     output {
-        File tumor_bam_data = "${normal_id}.bam"
-        File normal_bam_data = "${sample_id}.bam"
+        File tumor_bam_data = "${normal_id}.sorted.deduped.nochr.bam"
+        File normal_bam_data = "${sample_id}.sorted.deduped.nochr.bam"
     }
 
 }