test

tasks/VEP.wdl

@@ -23,43 +23,43 @@ task VEP {
     source /etc/profile
 
     #awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${sample_id}.vcf
-    
+
+    # Set the buffer_size based on the data size
+    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
+
+
     # Judge the SAMPLE info of vcf file
     tumor_id=`awk -F'\t' '{if($1~"^#CHROM"){print $10}}' ${vcf}`
     normal_id=`awk -F'\t' '{if($1~"^#CHROM"){print $11}}' ${vcf}`
-
+    
     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"
-      cp ${vcf} raw.vcf
+      cp ${vcf} ${sample_id}.tmp.vcf
     else
       SAMPLE_vcf2maf="--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
-
-
-    # Set the buffer_size based on the data size
-    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"
+      awk -F'\t' 'OFS="\t" {if($1!~"^##" && length($11)==0) $11=$10; print $0}' ${vcf} > ${sample_id}.tmp1.vcf
     fi
 
 
     # vcf2vcf: transfer into a standardized format
     echo "Transfer the VCF file into a standardized format..."
     perl ${vcf2maf_path}/vcf2vcf.pl \
-    --input-vcf $raw.vcf --output-vcf norm.vcf \
+    --input-vcf ${sample_id}.tmp1.vcf --output-vcf ${sample_id}.tmp2.vcf \
     $SAMPLE_vcf2vcf \
     --ref-fasta ${ref_dir}/${fasta}
     
     if [ $normal_id ]; then
-      cp $norm.vcf ${basename}.norm.vcf
+      cp ${sample_id}.tmp2.vcf ${basename}.norm.vcf
     else
-      cut -f 1,2,3,4,5,6,7,8,9,10 $norm.vcf > ${basename}.norm.vcf
+      cut -f 1,2,3,4,5,6,7,8,9,10 ${sample_id}.tmp2.vcf > ${basename}.norm.vcf
     
 
     # VEP annotation