vcf_concatenate_germline workflow edit

nf-core · Nov 27, 2024 · e877ed4 · e877ed4
1 parent af736b4
commit e877ed4
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git 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
@@ -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 ]
 }