Update: add annotation

tasks/VEP.wdl

 
     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}`
     normal_id=`awk -F'\t' '{if($1~"^#CHROM"){print $11}}' ${vcf}`
     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 \
     $SAMPLE_vcf2vcf \
     --ref-fasta ${ref_dir}/${fasta}
 
+    
     # VEP annotation
+    echo "VEP annotation..."
     perl ${vep_path}/vep --format vcf --vcf \
     --assembly ${ncbi_build} \
     --species ${species} \
     $buffer_size \
     --input_file ${basename}.norm.vcf --output_file ${basename}.vep.vcf
 
+    
     # vcf2maf
+    echo "vcf2maf..."
     perl ${vcf2maf_path}/vcf2maf.pl \
     --inhibit-vep \
     --input-vcf ${basename}.vep.vcf --output-maf ${basename}.maf \