From e2bc234a0417c9a1a65f2bebddb572ba3045d1d0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= <seb.schoenherr@gmail.com>
Date: Thu, 3 Oct 2024 09:12:31 +0200
Subject: [PATCH] Create tabix index to skip HTSJDK index creation

---
 modules/local/quality_control/quality_control_vcf.nf | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/modules/local/quality_control/quality_control_vcf.nf b/modules/local/quality_control/quality_control_vcf.nf
index dcca87c..37f6820 100644
--- a/modules/local/quality_control/quality_control_vcf.nf
+++ b/modules/local/quality_control/quality_control_vcf.nf
@@ -36,6 +36,18 @@ process QUALITY_CONTROL_VCF {
     set +e
     echo '${JsonOutput.toJson(params.refpanel)}' > reference-panel.json
 
+    # Verify if VCF files are valid
+    for vcf in $vcf_files; do
+        # Attempt to create the index using tabix
+        if ! output=\$(tabix -p vcf "\$vcf" 2>&1); then
+            echo ::group type=error
+            echo "The provided VCF file is malformed."
+            echo "Error: \$output"
+            echo ::endgroup::
+            exit 1
+        fi
+    done
+    
     # TODO: create directories in java
     mkdir ${chunksDir}
     mkdir ${metaFilesDir}