Update CHANGELOG

nf-core · Aug 8, 2024 · d5d3b98 · d5d3b98
1 parent 5f11686
commit d5d3b98
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 1 deletion.
diff --git 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
@@ -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