Alter: add filter parameter

defaults

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

inputs

@@ -9,6 +9,7 @@
   "{{ project_name }}.cache": "{{ cache }}",
   "{{ project_name }}.ncbi_build": "{{ ncbi_build }}",
   "{{ project_name }}.species": "{{ species }}",
+  "{{ project_name }}.only_pass": {{ only_pass | tojson }},
   "{{ project_name }}.vep_docker": "{{ vep_docker }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}"

tasks/vcf2maf.wdl

@@ -10,6 +10,7 @@ task vcf2maf {
   File cache
   String ncbi_build
   String species
+  Boolean only_pass
   String docker
   String cluster_config
   String disk_size
@@ -18,9 +19,16 @@ task vcf2maf {
   command <<<
     set -o pipefail
     set -e
-    nt=$(nproc)    
+    nt=$(nproc)
+
+    if [ only_pass ]; then
+    awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > input_vcf
+    else
+    cat ${vcf} > input_vcf
+    fi
+
     perl /opt/mskcc-vcf2maf/vcf2maf.pl \
-    --input-vcf ${vcf} --output-maf ${basename}.maf \
+    --input-vcf ${input_vcf} --output-maf ${basename}.maf \
     --tumor-id ${tumor_id} --normal-id ${normal_id} \
     --ref-fasta ${ref_dir}/${fasta} \
     --vep-path ${vep_path} \

workflow.wdl

@@ -12,6 +12,7 @@ workflow {{ project_name }} {
   File cache
   String ncbi_build
   String species
+  Boolean only_pass
   String vep_docker
   String cluster_config
   String disk_size
@@ -27,6 +28,7 @@ workflow {{ project_name }} {
     cache=cache,
     ncbi_build=ncbi_build,
     species=species,
+    only_pass=only_pass,
     docker=vep_docker,
     cluster_config=cluster_config,
     disk_size=disk_size