third commit

charger_test.csv

@@ -1,3 +0,0 @@
-sample_id,vep_vcf
-CBCGA274535.Haplotyper,oss://choppy-cromwell-result/test-choppy/CBCGA_filter_vep_charger_1_150_0903/1efaeacc-2441-447b-bc75-28c2f36bae98/call-filter_vep_annovar/glob-9a6c87b5232fb2ca5fafac9fc0f9b28e/CBCGA274535.Haplotyper.PASS.vep.filter.vcf
-

tasks/charger.wdl

@@ -15,13 +15,17 @@ task charger{
 	
         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/
-        charger -f ${vep_vcf} \
+        grep "#" ${vep_vcf} > ./input/$vep_input
+        grep -v "#" ${vep_vcf}|sed 's/\.0//' >> ./input/$vep_input
+
+        charger -f ./input/$vep_input \
             -o ./output/$vep_index.charger.tsv \
             -D ${inheritanceGeneList} \
             -l --mac-clinvar-tsv ${clinvar} \