Merge pull request #350 from nf-core/fix-star-index

Fix star index issues
nf-core · Aug 12, 2024 · 23fcbdb · 23fcbdb
2 parents 66221f6 + ed25fd5
commit 23fcbdb
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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))
 - Update modules ([#351](https://github.com/nf-core/scrnaseq/pull/351))
 
 ## v2.7.0 - 2024-06-03

diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -67,7 +67,8 @@ workflow SCRNASEQ {
     ch_salmon_index = params.salmon_index ? file(params.salmon_index) : []
 
     //star params
-    ch_star_index = params.star_index ? file(params.star_index) : []
+    star_index = params.star ? file(params.star_index, checkIfExists: true) : ( params.genome ? file( getGenomeAttribute('star'), checkIfExists: true ) : [] )
+    ch_star_index = [[id: star_index.baseName], star_index]
     star_feature = params.star_feature
 
     //cellranger params