From dfb2d1574d057b4503127f4ea7b564aa09aca03e Mon Sep 17 00:00:00 2001
From: tdanhorn <tdanhorn@fastmail.fm>
Date: Mon, 27 Jan 2025 11:17:44 -0700
Subject: [PATCH] Merge intervals for WES in GATK GenomicsDBImport (#1777)

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Running sarek with `--joint_germline` on WES samples with an intervals
file containing many thousands of targets causes GATK `GenomicsDBImport`
to create millions of files and run for several days without completing.
Adding the `--merge-intervals` option to that process fixes that. This
PR add the parameter conditional on the `--wes` pipeline parameter.

Closes #1776

---------

Co-authored-by: Thomas <thomas@ideapad5.local>
Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io>
---
 CHANGELOG.md                       | 1 +
 conf/modules/joint_germline.config | 4 +++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6f3161eb42..72195563fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [1767](https://github.com/nf-core/sarek/pull/1767) - Bump nf-schema version to 2.2.1
+- [1777](https://github.com/nf-core/sarek/pull/1777) - Merge intervals for WES in GATK GenomicsDBImport
 
 ### Fixed
 
diff --git a/conf/modules/joint_germline.config b/conf/modules/joint_germline.config
index 61a296721d..b3f5bffc8b 100644
--- 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