remove only_pass

defaults

@@ -6,7 +6,6 @@
   "vep_path": "/opt/vep/ensembl-vep",
   "species": "homo_sapiens_merged",
   "ncbi_build": "GRCh38",
-  "only_pass": true,
   "vcf2maf_path": "/opt/mskcc-vcf2maf", 
   "disk_size": "200",
   "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc"

inputs

@@ -7,7 +7,6 @@
   "{{ project_name }}.cache": "{{ cache }}",
   "{{ project_name }}.ncbi_build": "{{ ncbi_build }}",
   "{{ project_name }}.species": "{{ species }}",
-  "{{ project_name }}.only_pass": {{ only_pass | tojson }},
   "{{ project_name }}.vcf2maf_path": "{{ vcf2maf_path }}",
   "{{ project_name }}.vep_docker": "{{ vep_docker }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",

tasks/VEP.wdl

@@ -11,7 +11,6 @@ task VEP {
   File cache
   String ncbi_build
   String species
-  Boolean only_pass
   String vcf2maf_path
   String docker
   String cluster_config
@@ -24,7 +23,7 @@ task VEP {
     nt=$(nproc)
 
     awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${sample_id}.PASS.vcf
-    
+
     # Extract the BND variants from VCF
     # awk -F'\t' '{if(($1~"^#")||($8!~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.PASS.vcf > ${sample_id}.PASS.vcf2maf.vcf
     # awk -F'\t' '{if(($1~"^#")||($8~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.PASS.vcf > ${sample_id}.INPUT.VEP.vcf

workflow.wdl

@@ -10,7 +10,6 @@ workflow {{ project_name }} {
   File cache
   String ncbi_build
   String species
-  Boolean only_pass
   String vcf2maf_path
   String vep_docker
   String cluster_config
@@ -28,7 +27,6 @@ workflow {{ project_name }} {
     cache=cache,
     ncbi_build=ncbi_build,
     species=species,
-    only_pass=only_pass,
     vcf2maf_path=vcf2maf_path,
     docker=vep_docker,
     cluster_config=cluster_config,