test

tasks/VEP.wdl

@@ -52,14 +52,14 @@ task VEP {
     # 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 $raw.vcf --output-vcf norm.vcf \
     $SAMPLE_vcf2vcf \
     --ref-fasta ${ref_dir}/${fasta}
     
     if [ $normal_id ]; then
-      cp norm.vcf ${basename}.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
+      cut -f 1,2,3,4,5,6,7,8,9,10 $norm.vcf > ${basename}.norm.vcf
     
 
     # VEP annotation
@@ -76,7 +76,6 @@ task VEP {
     --fork $nt
     
 
-    
     # vcf2maf
     echo "vcf2maf..."
     perl ${vcf2maf_path}/vcf2maf.pl \
@@ -85,8 +84,8 @@ task VEP {
     $SAMPLE_vcf2maf \
     --ref-fasta ${ref_dir}/${fasta} \
     --ncbi-build ${ncbi_build} \
-    --species ${species} \
-    --vep-fork $nt
+    --species ${species}
+
   >>>
   
   runtime {