From d5d3b98b428e45a87b0ec1a6049bc2f1075df5cd Mon Sep 17 00:00:00 2001
From: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com>
Date: Thu, 8 Aug 2024 11:07:06 +0200
Subject: [PATCH] Update CHANGELOG

---
 CHANGELOG.md          | 1 +
 workflows/scrnaseq.nf | 8 +++++++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 63d5b532..401c15c9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 - Add support for 10XV4 chemistry ([#348](https://github.com/nf-core/scrnaseq/pull/348))
+- Fix issues with predefined STAR index ([#350](https://github.com/nf-core/scrnaseq/pull/350))
 
 ## v2.7.0 - 2024-06-03
 
diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
index 5c789c57..e09341e5 100644
--- a/workflows/scrnaseq.nf
+++ b/workflows/scrnaseq.nf
@@ -67,7 +67,13 @@ workflow SCRNASEQ {
     ch_salmon_index = params.salmon_index ? file(params.salmon_index) : []
 
     //star params
-    ch_star_index = params.star_index ? file(params.star_index) : []
+    if (params.star_index) {
+        ch_star_index = Channel.fromPath(params.star_index).map{f -> [[id:f.baseName], f] }
+    } else if (params.genome ) {
+        ch_star_index = Channel.fromPath(params.genomes[params.genome]["star"]).map{ f -> [[id:f.baseName], f] }
+    } else {
+        ch_star_index = []
+    }
     star_feature = params.star_feature
 
     //cellranger params