更新 'tasks/charger.wdl'

./input/${vep_index}.nochr.vcf

tasks/charger.wdl

@@ -19,9 +19,12 @@ task charger{
         vep_index=`echo ${vep_vcf}|awk -F "/" '{print $NF}'|sed 's/.vcf//'`
 
         echo ${sample_id}
+        
+        mkdir ./input/
         mkdir ./output/
+        sed 's/chr//' ${vep_vcf} > ./input/${vep_index}.nochr.vcf 
 
-        charger -f ${vep_vcf} \
+        charger -f ./input/${vep_index}.nochr.vcf \
             -o ./output/$vep_index.charger.tsv \
             -D --inheritanceGeneList ${inheritanceGeneList} \
             -l --mac-clinvar-tsv ${clinvar} \