Merge intervals for WES in GATK GenomicsDBImport

nf-core · Jan 22, 2025 · a35cafc · a35cafc
1 parent 52b3fff
commit a35cafc
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/conf/modules/joint_germline.config b/conf/modules/joint_germline.config
@@ -16,7 +16,9 @@
 process {
 
     withName: 'GATK4_GENOMICSDBIMPORT' {
-        ext.args   = { '--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' }
+        ext.args   = { params.wes ?
+                            '--merge-input-intervals --genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' :
+                            '--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' }
         ext.prefix = { "${meta.intervals_name}.joint" }
         publishDir = [
             enabled: false