From c3b4bcfa1cd824c6359f58c2639294f547bbeb72 Mon Sep 17 00:00:00 2001
From: Jaeyeon Lee <Jaeyeon.Lee@bcm.edu>
Date: Wed, 20 Nov 2024 15:51:54 -0600
Subject: [PATCH] Validate VCF First Before Preprocessing

---
 main.nf  | 16 +++++++++++++++-
 test.txt |  0
 2 files changed, 15 insertions(+), 1 deletion(-)
 create mode 100644 test.txt

diff --git a/main.nf b/main.nf
index 3ecd8f1..bff316c 100644
--- a/main.nf
+++ b/main.nf
@@ -74,6 +74,19 @@ showUsage()
 showVersion()
 validateInputParams()
 
+process VALIDATE_VCF {
+    container 'quay.io/biocontainers/vcftools:0.1.16--pl5321hdcf5f25_11'
+
+    input:
+    path vcf
+
+    output:
+    path "$vcf", emit: vcf
+
+    """
+    vcf-validator $vcf
+    """
+}
 
 // Process to handle the VCF file
 process NORMALIZE_VCF {
@@ -654,7 +667,8 @@ workflow PHRANK_SCORING {
 }
 
 workflow {
-    NORMALIZE_VCF(params.input_vcf)
+    VALIDATE_VCF(params.input_vcf)
+    NORMALIZE_VCF(VALIDATE_VCF.out.vcf)
     BUILD_REFERENCE_INDEX()
 
     VCF_PRE_PROCESS(
diff --git a/test.txt b/test.txt
new file mode 100644
index 0000000..e69de29