更新 'tasks/samtools.wdl'

tasks/samtools.wdl

 task samtools {
     File bam_file
     String bam_id=basename(bam_file)
-
+    String sample_id
     String docker
     String cluster
     String disk_size
     command <<<
        set -o pipefail
        set -e
-
-       cp ${bam_file} ${bam_id}       
-       samtools index ${bam_file}
+                  
+       mkdir -p ${sample_id}/data
+       cp ${bam_file} ${sample_id}/data/${bam_id}       
+       samtools index ${sample_id}/data/${bam_id}
 
     >>>