From 94211c11c9d86c762a8a1984a334567c39b47828 Mon Sep 17 00:00:00 2001
From: Ira Cooke <iracooke@gmail.com>
Date: Mon, 23 Sep 2024 15:34:59 +1000
Subject: [PATCH] Keep index from haplotype caller

---
 modules/gatk.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/gatk.nf b/modules/gatk.nf
index d486a86..0cfcb07 100644
--- a/modules/gatk.nf
+++ b/modules/gatk.nf
@@ -154,7 +154,7 @@ process gatk_haplotype_caller {
 
     script:
     def args = task.ext.args ?: ''
-    def outfile = "${bam.baseName}.g.vcf.gz"
+    def outfile = "${bam.baseName}.g.vcf.gz*"
 
     """