Fixbug: cp data

tasks/VEP.wdl

@@ -31,7 +31,7 @@ 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
+      cp ${vcf} raw.vcf
     else
       SAMPLE_vcf2maf="--tumor-id $tumor_id"
       # Add a column and remove it after vcf2vcf
@@ -57,7 +57,7 @@ task VEP {
     --ref-fasta ${ref_dir}/${fasta}
     
     if [ $normal_id ]; then
-      ${basename}.norm.vcf=norm.vcf
+      cp norm.vcf ${basename}.norm.vcf
     else
       cut -f 1,2,3,4,5,6,7,8,9,10 norm.vcf > ${basename}.norm.vcf