更新 'tasks/battenberg.wdl'

tasks/battenberg.wdl

@@ -15,14 +15,14 @@ task battenberg {
         cp ${normal_bam} ./${normal_id}.bam
         cp ${tumor_bam} ./${sample_id}.bam
 
-        samtools view -h -@ 28 -o ${normal_id}.sorted.deduped.sam ./${normal_id}.bam
-        samtools view -h -@ 28 -o ${sample_id}.sorted.deduped.sam ./${sample_id}.bam
+        #samtools view -h -@ 28 -o ${normal_id}.sorted.deduped.sam ./${normal_id}.bam
+        #samtools view -h -@ 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
+       # 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
+       # 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
    
 
 
@@ -36,8 +36,8 @@ task battenberg {
     }
 
     output {
-        File tumor_bam_data = "${sample_id}.sorted.deduped.nochr.bam"
-        File normal_bam_data = "${normal_id}.sorted.deduped.nochr.bam"
+        File tumor_bam_data = "${normal_id}.bam"
+        File normal_bam_data = "${sample_id}.bam"
     }
 
 }