Update: remove # line

tasks/VEP.wdl

@@ -44,36 +44,7 @@ task VEP {
       buffer_size="--buffer_size 500"
     fi
 
-    # Extract the BND variants from VCF
-    # awk -F'\t' '{if(($1~"^#")||($8!~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.PASS.vcf > ${sample_id}.PASS.vcf2maf.vcf
-    # awk -F'\t' '{if(($1~"^#")||($8~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.PASS.vcf > ${sample_id}.INPUT.VEP.vcf
-
-    # vcf2maf
-    # perl ${vcf2maf_path}/vcf2maf.pl \
-    # --input-vcf ${sample_id}.PASS.vcf2maf.vcf --output-maf ${basename}.maf \
-    # --tumor-id ${tumor_id} --normal-id ${normal_id} \
-    # --ref-fasta ${ref_dir}/${fasta} \
-    # --vep-path ${vep_path} \
-    # --vep-data ${cache} \
-    # --ncbi-build ${ncbi_build} \
-    # --species ${species} \
-    # --vep-fork $nt
-
     # vep
-    # perl ${vep_path}/vep \
-    # --input_file ${basename}.PASS.vcf --output_file ${basename}.PASS.vep.vcf \
-    # --fasta ${ref_dir}/${fasta} \
-    # --dir ${cache} \
-    # --assembly ${ncbi_build} \
-    # --species ${species} \
-    # --fork $nt \
-    # --format vcf --vcf \
-    # --no_progress \
-    # --no_stats \
-    # $buffer_size \
-    # --sift b \
-    # --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --force_overwrite --offline --pubmed --regulatory
-    
     perl ${vep_path}/vep --format vcf --vcf \
     --assembly $ncbi_build \
     --species ${species} \