更新 'tasks/samtools.wdl'

tasks/samtools.wdl

@@ -7,11 +7,9 @@ task samtools {
 
 
     command <<<
-       set -o pipefail
-       set -e        
-       mkdir -p /cromwell_root/tmp/
-       cp ${bam_file} /cromwell_root/tmp/
-       /opt/conda/bin/samtools index -b /cromwell_root/tmp/${bam_id}
+       samtools index --help
+       samtools index -b ${bam_file} > ./${bam_id}.bai
+       cp ${bam_file} ./                               
     >>>
 
     runtime {