更新 'tasks/battenberg.wdl'

${normal_id}.sorted.deduped.nochr.bam

tasks/battenberg.wdl

@@ -15,9 +15,14 @@ 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
+        samtools view -h -@ 16 -o ${normal_id}.sorted.deduped.sam ./${normal_id}.bam
+        samtools view -h -@ 16 -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 -@ 16 -o ${normal_id}.sorted.deduped.nochr.bam ${normal_id}.sorted.deduped.sam
+        samtools sort -@ 16 -o ${sample_id}.sorted.deduped.nochr.bam ${sample_id}.sorted.deduped.sam
 
     >>>