rename output

tasks/VEP.wdl

     set -e
     nt=$(nproc)
 
-    awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${sample_id}.PASS.vcf
+    awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${basename}.PASS.vcf
 
     # 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
 
     # vep
     perl ${vep_path}/vep \
-    --input_file ${sample_id}.PASS.vcf --output_file ${basename}.vep.vcf \
+    --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 5000 --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
+    --no_progress \
+    --no_stats \
+    --buffer_size 5000 \
+    --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
 
     # vcf2maf
     perl ${vcf2maf_path}/vcf2maf.pl \
     --inhibit-vep \
-    --input-vcf ${basename}.vep.vcf --output-maf ${basename}.maf \
+    --input-vcf ${basename}.PASS.vep.vcf --output-maf ${basename}.PASS.maf \
     --tumor-id ${tumor_id} --normal-id ${normal_id} \
     --ref-fasta ${ref_dir}/${fasta} \
     --vep-fork $nt
   }
 
   output {
-    File input_vcf = "${sample_id}.PASS.vcf"
-    File vep_vcf = "${basename}.vep.vcf"
-    File maf = "${basename}.maf"
+    File input_vcf = "${basename}.PASS.vcf"
+    File vep_vcf = "${basename}.PASS.vep.vcf"
+    File maf = "${basename}.PASS.maf"
   }
 }