From e877ed48c4d97b02b2e3caa4b1e4fea9fa198965 Mon Sep 17 00:00:00 2001
From: Patricie34 <patricie.johnova@email.cz>
Date: Wed, 27 Nov 2024 13:36:40 +0100
Subject: [PATCH] vcf_concatenate_germline workflow edit

---
 conf/modules/post_variant_calling.config            | 4 ++--
 subworkflows/local/vcf_concatenate_germline/main.nf | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/modules/post_variant_calling.config b/conf/modules/post_variant_calling.config
index 92b4cb9e4d..742e0c03f9 100644
--- a/conf/modules/post_variant_calling.config
+++ b/conf/modules/post_variant_calling.config
@@ -36,7 +36,7 @@ process {
     }
 
     withName: 'VCFS_NORM_SORT' {
-        ext.prefix = { "${meta.id}.norm" }
+        ext.prefix = { "${meta.id}.${meta.variantcaller}.norm" }
         ext.when   = { params.normalize_vcfs }
         publishDir = [
             mode: params.publish_dir_mode,
@@ -73,7 +73,7 @@ process {
     }
 
     withName: 'TABIX_VCFS_NORM_SORT'{
-        ext.prefix = { "${meta.id}.norm" }
+        ext.prefix = { "${meta.id}.${meta.variantcaller}.norm" }
         ext.when   = { params.normalize_vcfs }
         publishDir = [
             mode: params.publish_dir_mode,
diff --git a/subworkflows/local/vcf_concatenate_germline/main.nf b/subworkflows/local/vcf_concatenate_germline/main.nf
index a38197a8f3..3b80337e7f 100644
--- a/subworkflows/local/vcf_concatenate_germline/main.nf
+++ b/subworkflows/local/vcf_concatenate_germline/main.nf
@@ -36,7 +36,7 @@ workflow CONCATENATE_GERMLINE_VCFS {
     versions = versions.mix(TABIX_GERMLINE_VCFS_CONCAT_SORT.out.versions)
 
     emit:
-    vcfs = germline_vcfs_with_tbis // concatenated vcfs
+    vcfs = GERMLINE_VCFS_CONCAT_SORT.out.vcf // concatenated vcfs
 
     versions // channel: [ versions.yml ]
 }