From 13833c39c870dc3046983e4dbb0d2f554440cc28 Mon Sep 17 00:00:00 2001
From: Nikhil Kumar <nikhilkumar516@gmail.com>
Date: Wed, 12 Jul 2023 13:54:59 -0400
Subject: [PATCH] Fixed typo in num lines check

---
 cwl/samples_fillout_workflow.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cwl/samples_fillout_workflow.cwl b/cwl/samples_fillout_workflow.cwl
index 3e9717a..919c526 100644
--- a/cwl/samples_fillout_workflow.cwl
+++ b/cwl/samples_fillout_workflow.cwl
@@ -137,7 +137,7 @@ steps:
                 fasta="${ return inputs.ref_fasta.path; }"
                 vcf="${ return inputs.targets_vcf.path }"
                 fillout_vcf="fillout.vcf"
-                num_lines="\$(grep -v '^[#]' \${input_maf} | wc -l)"
+                num_lines="\$(grep -v '^[#]' \${vcf} | wc -l)"
                 more_than_zero="\$(( \${num_lines} > 0))"
                 if [ "\${more_than_zero}" == "1" ]
                 then