From c450b08a75cda8878876ccbbe42493d6774397bd Mon Sep 17 00:00:00 2001
From: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 3 Mar 2022 11:54:07 +0100
Subject: [PATCH] separate gvcf and vcf in output channels (#1371)

* separate gvcf and vcf in output channels

* regex not working, just using prefix now
---
 modules/deepvariant/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/deepvariant/main.nf b/modules/deepvariant/main.nf
index c5e81997..8e5f10df 100644
--- a/modules/deepvariant/main.nf
+++ b/modules/deepvariant/main.nf
@@ -17,8 +17,8 @@ process DEEPVARIANT {
     path(fai)
 
     output:
-    tuple val(meta), path("*.vcf.gz") ,  emit: vcf
-    tuple val(meta), path("*g.vcf.gz"),  emit: gvcf
+    tuple val(meta), path("${prefix}.vcf.gz") ,  emit: vcf
+    tuple val(meta), path("${prefix}.g.vcf.gz"),  emit: gvcf
     path "versions.yml"               ,  emit: versions
 
     when:
@@ -26,7 +26,7 @@ process DEEPVARIANT {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     def regions = intervals ? "--regions ${intervals}" : ""
 
     """