Update: add PASS filter option

defaults

   "tnseq": false,
   "tnscope": false,
   "varscan": false,
-  "annovar": false
+  "annovar": false,
+  "only_pass": true
 }

inputs

   "{{ project_name }}.tnseq": {{ tnseq | tojson }},
   "{{ project_name }}.tnscope": {{ tnscope | tojson }},
   "{{ project_name }}.varscan": {{ varscan | tojson }},
-  "{{ project_name }}.annovar": {{ annovar | tojson }}
+  "{{ project_name }}.annovar": {{ annovar | tojson }},
+  "{{ project_name }}.only_pass": {{ only_pass | tojson }}
 }

tasks/ANNOVAR.wdl

   String basename = basename(vcf,".vcf")
   String hg
   File annovar_database
+  Boolean only_pass
   String docker
   String cluster_config
   String disk_size
     set -e
     nt=$(nproc)
 
+    if [ only_pass ]; then
+      awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${sample_id}.INPUT.vcf
+    else
+      cp ${vcf} ${sample_id}.INPUT.vcf
+    fi
+
     if [ ${hg} == "hg38" ]; then
-    /installations/annovar/table_annovar.pl ${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 ${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
     fi
 
     if [ ${hg} == "hg19" ]; then
-    /installations/annovar/table_annovar.pl ${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 ${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
     fi
   >>>
   

workflow.wdl

   Boolean varscan
 
   Boolean annovar
+  Boolean only_pass
 
   if (tumor_fastq_1!= "") {
     call mapping.mapping as tumor_mapping {
         input:
         vcf=TNseq.TNseq_vcf,
         hg=hg,
+        only_pass=only_pass,
         annovar_database=annovar_database,
         docker=annovar_docker,
         cluster_config=cluster_config,
         input:
         vcf=TNscope.TNscope_vcf,
         hg=hg,
+        only_pass=only_pass,
         annovar_database=annovar_database,
         docker=annovar_docker,
         cluster_config=cluster_config,
         input:
         vcf=somaticFilter.varscan_somatic_filter,
         hg=hg,
+        only_pass=only_pass,
         annovar_database=annovar_database,
         docker=annovar_docker,
         cluster_config=cluster_config,