Fixbug: vcf2vcf need --vcf-normal-id

tasks/VEP.wdl

@@ -31,9 +31,12 @@ task VEP {
     if [ $normal_id ]; then
       SAMPLE_vcf2maf="--tumor-id $tumor_id --normal-id $normal_id"
       SAMPLE_vcf2vcf="--vcf-tumor-id $tumor_id --vcf-normal-id $normal_id"
+      ${vcf} > raw.vcf
     else
       SAMPLE_vcf2maf="--tumor-id $tumor_id"
-      SAMPLE_vcf2vcf="--vcf-tumor-id $tumor_id"
+      # Add a column and remove it after vcf2vcf
+      SAMPLE_vcf2vcf="--vcf-tumor-id $tumor_id --vcf-normal-id $tumor_id"
+      awk -F'\t' 'OFS="\t" {if($1!~"^##" && length($11)==0) $11=$10; print $0}' ${vcf} > raw.vcf
     fi
 
 
@@ -49,14 +52,20 @@ task VEP {
     # vcf2vcf: transfer into a standardized format
     echo "Transfer the VCF file into a standardized format..."
     perl ${vcf2maf_path}/vcf2vcf.pl \
-    --input-vcf ${vcf} --output-vcf ${basename}.norm.vcf \
+    --input-vcf raw.vcf --output-vcf norm.vcf \
     $SAMPLE_vcf2vcf \
     --ref-fasta ${ref_dir}/${fasta}
-
     
+    if [ $normal_id ]; then
+      ${basename}.norm.vcf=norm.vcf
+    else
+      cut -f 1,2,3,4,5,6,7,8,9,10 norm.vcf > ${basename}.norm.vcf
+    
+
     # VEP annotation
     echo "VEP annotation..."
     perl ${vep_path}/vep --format vcf --vcf \
+    --input_file ${basename}.norm.vcf --output_file ${basename}.vep.vcf \
     --assembly ${ncbi_build} \
     --species ${species} \
     --everything --af_exac \
@@ -64,8 +73,8 @@ task VEP {
     --cache --dir_cache ${cache} \
     --fasta ${ref_dir}/${fasta} \
     $buffer_size \
-    --fork $nt \
-    --input_file ${basename}.norm.vcf --output_file ${basename}.vep.vcf
+    --fork $nt
+    
 
     
     # vcf2maf