更新 'tasks/battenberg.wdl'

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

tasks/battenberg.wdl

@@ -15,8 +15,11 @@ task battenberg {
         cp ${normal_bam} ./${normal_id}.bam
         cp ${tumor_bam} ./${sample_id}.bam
 
-        /opt/conda/envs/TREC/bin/samtools view -h -@ 16 -o ${normal_id}.sorted.deduped.sam ./${normal_id}.bam
+        /opt/conda/envs/TREC/bin/samtools view -h ./${normal_id}.bam |sed 's/chr//g'|samtools view  -bS -o ./${normal_id}.sorted.deduped.nochr.bam
+        /opt/conda/envs/TREC/bin/samtools view -h ./${sample_id}.bam |sed 's/chr//g'|samtools view  -bS -o ./${sample_id}.sorted.deduped.nochr.bam
 
+        samtools index  ./${normal_id}.sorted.deduped.nochr.bam
+        samtools index  ./${sample_id}.sorted.deduped.nochr.bam
     >>>
 
     runtime {
@@ -27,7 +30,10 @@ task battenberg {
     }
 
     output {
-        File normal_bam_data = "${normal_id}.sorted.deduped.sam"
+        File normal_bam_data = "${normal_id}.sorted.deduped.nochr.bam"
+        File normal_bai_data = "${normal_id}.sorted.deduped.nochr.bam.bai"
+        File tumor_bam_data = "${sample_id}.sorted.deduped.nochr.bam"
+        File tumor_bai_data = "${sample_id}.sorted.deduped.nochr.bam.bai"
     }
 
 }