Alter: add filter parameter

tasks/vcf2maf.wdl

@@ -22,13 +22,13 @@ 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} > INPUT.vcf
     else
-    cat ${vcf} > input_vcf
+      cp ${vcf} INPUT.vcf
     fi
 
     perl /opt/mskcc-vcf2maf/vcf2maf.pl \
-    --input-vcf $input_vcf --output-maf ${basename}.maf \
+    --input-vcf INPUT.vcf --output-maf ${basename}.maf \
     --tumor-id ${tumor_id} --normal-id ${normal_id} \
     --ref-fasta ${ref_dir}/${fasta} \
     --vep-path ${vep_path} \