From 0c9d5ff8d716c0e50d2c4d1349851d1468d3c54c Mon Sep 17 00:00:00 2001
From: kmhzamir <144998908+kmhzamir@users.noreply.github.com>
Date: Thu, 5 Feb 2026 08:24:12 +0800
Subject: [PATCH] Update main.nf

avoid override issue for input and output file because of same file name
---
 modules/nf-core/gatk4/preprocessintervals/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/gatk4/preprocessintervals/main.nf b/modules/nf-core/gatk4/preprocessintervals/main.nf
index 3d63502..5686bda 100644
--- a/modules/nf-core/gatk4/preprocessintervals/main.nf
+++ b/modules/nf-core/gatk4/preprocessintervals/main.nf
@@ -15,7 +15,7 @@ process GATK4_PREPROCESSINTERVALS {
     tuple val(meta5), path(exclude_intervals)
 
     output:
-    tuple val(meta), path("*.interval_list"), emit: interval_list
+    tuple val(meta), path("*.preprocessed.interval_list"), emit: interval_list
     path "versions.yml",                      emit: versions
 
     when:
@@ -41,7 +41,7 @@ process GATK4_PREPROCESSINTERVALS {
         ${include_command} \\
         ${exclude_command} \\
         --reference ${fasta} \\
-        --output ${prefix}.interval_list \\
+        --output ${prefix}.preprocessed.interval_list \\
         ${args}
 
     cat <<-END_VERSIONS > versions.yml