Update: remove only_pass

defaults

   "varscan": false,
   "annovar": false,
   "vep": false,
-  "only_pass": true,
   "input_fastq": false,
   "input_bam": false
 }

inputs

   "{{ project_name }}.tnscope": {{ tnscope | tojson }},
   "{{ project_name }}.varscan": {{ varscan | tojson }},
   "{{ project_name }}.annovar": {{ annovar | tojson }},
-  "{{ project_name }}.only_pass": {{ only_pass | tojson }},
   "{{ project_name }}.vep": {{ vep | tojson }},
   "{{ project_name }}.input_fastq": {{ input_fastq | tojson }},
   "{{ project_name }}.input_bam": {{ input_bam | 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} > INPUT.vcf
-    else
-      cp ${vcf} INPUT.vcf
-    fi
-
     if [ ${hg} == "hg38" ]; then
-    /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \
+    /installations/annovar/table_annovar.pl ${vcf} \
     ${annovar_database} -buildver ${hg} \
     -out ${basename} -remove \
     -protocol refGene,ensGene,knownGene,rmsk,cytoBand,genomicSuperDups,esp6500siv2_all,ALL.sites.2015_08,AFR.sites.2015_08,AMR.sites.2015_08,EAS.sites.2015_08,EUR.sites.2015_08,SAS.sites.2015_08,avsnp147,dbnsfp33a,clinvar_20210501,gnomad_genome,dbscsnv11,dbnsfp31a_interpro \
     fi
 
     if [ ${hg} == "hg19" ]; then
-    /installations/annovar/table_annovar.pl ${basename}.PASS.vcf \
+    /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 \

tasks/TNscope.wdl

     --dbsnp ${dbsnp_dir}/${dbsnp} \
     $PON \
     ${sample}.TNscope.vcf
+
+    awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${sample}.TNscope.vcf > ${sample}.TNscope.PASS.vcf
   >>>
 
   runtime {
   }
 
   output {
+    File TNscope_pass_vcf="${sample}.TNscope.PASS.vcf"
     File TNscope_vcf= "${sample}.TNscope.vcf"
     File TNscope_vcf_index = "${sample}.TNscope.vcf.idx"
   }

tasks/TNseq.wdl

     --tumor_segments ${sample}.contamination.segments \
     --orientation_priors ${sample}.orientation \
     ${sample}.TNseq.filter.vcf
+    
+    awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${sample}.TNseq.filter.vcf > ${sample}.TNseq.filter.PASS.vcf
   >>>
 
   runtime {
   }
 
   output {
+    File TNseq_pass_vcf='${sample}.TNseq.filter.PASS.vcf'
     File TNseq_filter_vcf='${sample}.TNseq.filter.vcf'
     File TNseq_filter_vcf_index = "${sample}.TNseq.filter.vcf.idx"
     File TNseq_vcf = "${sample}.TNseq.vcf"

tasks/VEP.wdl

     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
-
     # Define ncbi_build
     if [ hg == "hg19" ]; then
       ncbi_build="GRCh37"
     fi
 
     # Extract the BND variants from VCF
-    awk -F'\t' '{if(($1~"^#")||($8!~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.INPUT.vcf > ${sample_id}.INPUT.vcf2maf.vcf
-    awk -F'\t' '{if(($1~"^#")||($8~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.INPUT.vcf > ${sample_id}.INPUT.VEP.vcf
+    awk -F'\t' '{if(($1~"^#")||($8!~".*SVTYPE=BND.*")){print $0}}' ${vcf} > ${sample_id}.INPUT.vcf2maf.vcf
+    awk -F'\t' '{if(($1~"^#")||($8~".*SVTYPE=BND.*")){print $0}}' ${vcf} > ${sample_id}.INPUT.VEP.vcf
 
     # vcf2maf
     perl ${vcf2maf_path}/vcf2maf.pl \
   }
 
   output {
-    File input_vcf = "${sample_id}.INPUT.vcf"
     File maf = "${basename}.${hg}.maf"
     File bnd_vep = "${basename}.BND.VEP.txt"
   }

workflow.wdl

 
   Boolean annovar
   Boolean vep
-  Boolean only_pass
 
   if (input_fastq) {
     if (tumor_fastq_1!= "") {
       if (annovar) {
         call ANNOVAR.ANNOVAR as TNseq_annovar {
           input:
-          vcf=TNseq.TNseq_filter_vcf,
+          vcf=TNseq.TNseq_pass_vcf,
           hg=hg,
-          only_pass=only_pass,
           annovar_database=annovar_database,
           docker=annovar_docker,
           cluster_config=cluster_config,
       if (vep) {
         call VEP.VEP as TNseq_VEP {
           input: 
-          vcf=TNseq.TNseq_filter_vcf,
+          vcf=TNseq.TNseq_pass_vcf,
           hg=hg,
-          only_pass=only_pass,
           sample_id=sample_id,
           tumor_id=sample_id + ".T",
           normal_id=sample_id + ".N",
       if (annovar) {
         call ANNOVAR.ANNOVAR as TNscope_annovar {
           input:
-          vcf=TNscope.TNscope_vcf,
+          vcf=TNscope.TNscope_pass_vcf,
           hg=hg,
-          only_pass=only_pass,
           annovar_database=annovar_database,
           docker=annovar_docker,
           cluster_config=cluster_config,
       if (vep) {
         call VEP.VEP as TNscope_VEP {
           input: 
-          vcf=TNscope.TNscope_vcf,
+          vcf=TNscope.TNscope_pass_vcf,
           hg=hg,
-          only_pass=only_pass,
           sample_id=sample_id,
           tumor_id=sample_id + ".T",
           normal_id=sample_id + ".N",
           input:
           vcf=somaticFilter.varscan_somatic_filter,
           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,
           sample_id=sample_id,
           tumor_id=sample_id + ".T",
           normal_id=sample_id + ".N",
       if (annovar) {
         call ANNOVAR.ANNOVAR as TNseq_annovar_fb {
           input:
-          vcf=TNseq_fb.TNseq_filter_vcf,
+          vcf=TNseq_fb.TNseq_pass_vcf,
           hg=hg,
-          only_pass=only_pass,
           annovar_database=annovar_database,
           docker=annovar_docker,
           cluster_config=cluster_config,
       if (vep) {
         call VEP.VEP as TNseq_VEP_fb {
           input: 
-          vcf=TNseq_fb.TNseq_filter_vcf,
+          vcf=TNseq_fb.TNseq_pass_vcf,
           hg=hg,
-          only_pass=only_pass,
           sample_id=sample_id,
           tumor_id=sample_id + ".T",
           normal_id=sample_id + ".N",
       if (annovar) {
         call ANNOVAR.ANNOVAR as TNscope_annovar_fb {
           input:
-          vcf=TNscope_fb.TNscope_vcf,
+          vcf=TNscope_fb.TNscope_pass_vcf,
           hg=hg,
-          only_pass=only_pass,
           annovar_database=annovar_database,
           docker=annovar_docker,
           cluster_config=cluster_config,
       if (vep) {
         call VEP.VEP as TNscope_VEP_fb {
           input: 
-          vcf=TNscope_fb.TNscope_vcf,
+          vcf=TNscope_fb.TNscope_pass_vcf,
           hg=hg,
-          only_pass=only_pass,
           sample_id=sample_id,
           tumor_id=sample_id + ".T",
           normal_id=sample_id + ".N",
           input:
           vcf=somaticFilter_fb.varscan_somatic_filter,
           hg=hg,
-          only_pass=only_pass,
           annovar_database=annovar_database,
           docker=annovar_docker,
           cluster_config=cluster_config,
           input: 
           vcf=somaticFilter_fb.varscan_somatic_filter,
           hg=hg,
-          only_pass=only_pass,
           sample_id=sample_id,
           tumor_id=sample_id + ".T",
           normal_id=sample_id + ".N",