更新 'tasks/battenberg.wdl'

${normal_id}.sorted.deduped.sam

tasks/battenberg.wdl

@@ -15,8 +15,7 @@ task battenberg {
         cp ${normal_bam} ./${normal_id}.bam
         cp ${tumor_bam} ./${sample_id}.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
+        /opt/conda/envs/batternberg/bin/samtools view -h -@ 16 -o ${normal_id}.sorted.deduped.sam ./${normal_id}.bam
 
     >>>
 
@@ -28,8 +27,7 @@ task battenberg {
     }
 
     output {
-        File tumor_bam_data = "${normal_id}.sorted.deduped.sam"
-        File normal_bam_data = "${sample_id}.sorted.deduped.sam"
+        File normal_bam_data = "${normal_id}.sorted.deduped.sam"
     }
 
 }