Fixbug: ANNOVAR

tasks/ANNOVAR.wdl

@@ -16,17 +16,17 @@ task ANNOVAR {
     nt=$(nproc)
 
     if [ only_pass ]; then
-      awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${sample_id}.INPUT.vcf
+      awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > INPUT.vcf
     else
-      cp ${vcf} ${sample_id}.INPUT.vcf
+      cp ${vcf} INPUT.vcf
     fi
 
     if [ ${hg} == "hg38" ]; then
-      /installations/annovar/table_annovar.pl ${sample_id}.INPUT.vcf ${annovar_database} -buildver ${hg} -out ${basename} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+      /installations/annovar/table_annovar.pl INPUT.vcf ${annovar_database} -buildver ${hg} -out ${basename} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
     fi
 
     if [ ${hg} == "hg19" ]; then
-      /installations/annovar/table_annovar.pl ${sample_id}.INPUT.vcf ${annovar_database} -buildver ${hg} -out ${basename} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,snp138,cosmic78,intervar_20170202,popfreq_all_20150413,clinvar_20190305 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+      /installations/annovar/table_annovar.pl INPUT.vcf ${annovar_database} -buildver ${hg} -out ${basename} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,snp138,cosmic78,intervar_20170202,popfreq_all_20150413,clinvar_20190305 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
     fi
   >>>