Alter: add output vcf

tasks/vcf2maf.wdl

@@ -1,6 +1,7 @@
 task vcf2maf {
 
   File vcf
+  String sample_id
   String basename = basename(vcf,".vcf")
   String tumor_id
   String normal_id
@@ -22,13 +23,13 @@ task vcf2maf {
     nt=$(nproc)
 
     if [ only_pass ]; then
-      awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > INPUT.vcf
+      awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${sample_id}.INPUT.vcf
     else
-      cp ${vcf} INPUT.vcf
+      cp ${vcf} ${sample_id}.INPUT.vcf
     fi
 
     perl /opt/mskcc-vcf2maf/vcf2maf.pl \
-    --input-vcf INPUT.vcf --output-maf ${basename}.maf \
+    --input-vcf ${sample_id}.INPUT.vcf --output-maf ${basename}.maf \
     --tumor-id ${tumor_id} --normal-id ${normal_id} \
     --ref-fasta ${ref_dir}/${fasta} \
     --vep-path ${vep_path} \
@@ -46,6 +47,7 @@ task vcf2maf {
   }
 
   output {
+    File vcf = "${sample_id}.INPUT.vcf"
     File maf = "${basename}.maf"
   }
 }

workflow.wdl

@@ -20,6 +20,7 @@ workflow {{ project_name }} {
   call vcf2maf.vcf2maf as vcf2maf {
     input: 
     vcf=vcf,
+    sample_id=sample_id,
     tumor_id=tumor_id,
     normal_id=normal_id,
     ref_dir=ref_dir,