4 commit

tasks/charger.wdl

         set -o pipefail
         set -e
         
-        vep_input=`echo ${vep_vcf}|awk -F "/" '{print $NF}'`
         vep_index=`echo ${vep_vcf}|awk -F "/" '{print $NF}'|sed 's/.vcf//'`
 
         echo ${sample_id}
-        mkdir ./input/
         mkdir ./output/
-        grep "#" ${vep_vcf} > ./input/$vep_input
-        grep -v "#" ${vep_vcf}|sed 's/\.0//' >> ./input/$vep_input
 
-        charger -f ./input/$vep_input \
+        charger -f ${vep_vcf} \
             -o ./output/$vep_index.charger.tsv \
             -D ${inheritanceGeneList} \
             -l --mac-clinvar-tsv ${clinvar} \