Update: remove filtering process

tasks/VEP.wdl

@@ -22,7 +22,7 @@ task VEP {
 
     source /etc/profile
 
-    awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${sample_id}.vcf
+    #awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${sample_id}.vcf
     
     # Judge the SAMPLE info of vcf file
     tumor_id=`awk -F'\t' '{if($1~"^#CHROM"){print $10}}' ${vcf}`
@@ -36,18 +36,20 @@ task VEP {
       SAMPLE_vcf2vcf="--vcf-tumor-id $tumor_id"
     fi
 
+
     # Set the buffer_size based on the data size
-    nrow=`awk -F'\t' '{if($1~"^chr"){print $0}}' ${sample_id}.vcf | wc -l`
+    nrow=`awk -F'\t' '{if($1~"^chr"){print $0}}' ${vcf} | wc -l`
     if [ $nrow -lt 5000 ]; then
       buffer_size="--buffer_size 5000"
     else
       buffer_size="--buffer_size 1000"
     fi
 
+
     # vcf2vcf: transfer into a standardized format
     echo "Transfer the VCF file into a standardized format..."
     perl ${vcf2maf_path}/vcf2vcf.pl \
-    --input-vcf ${sample_id}.vcf --output-vcf ${basename}.norm.vcf \
+    --input-vcf ${vcf} --output-vcf ${basename}.norm.vcf \
     $SAMPLE_vcf2vcf \
     --ref-fasta ${ref_dir}/${fasta}
 
@@ -62,6 +64,7 @@ task VEP {
     --cache --dir_cache ${cache} \
     --fasta ${ref_dir}/${fasta} \
     $buffer_size \
+    --fork $nt \
     --input_file ${basename}.norm.vcf --output_file ${basename}.vep.vcf