更新 'tasks/samtools.wdl'

tasks/samtools.wdl

@@ -11,9 +11,9 @@ task samtools {
        set -o pipefail
        set -e
                   
-       mkdir -p ${sample_id}/data
-       cp ${bam_file} ${sample_id}/data/${bam_id}       
-       samtools index ${sample_id}/data/${bam_id}
+       mkdir -p /cromwell_root/tmp/
+       cp ${bam_file} /cromwell_root/tmp/
+       /opt/conda/bin/samtools index /cromwell_root/tmp/${bam_id} > $(bam_id).bai
 
     >>>