Merge pull request #289 from WackerO/dev

small gprofiler2 bugfix
nf-core · Oct 18, 2024 · e02479f · e02479f
2 parents 83699b7 + 7e5cf9f
commit e02479f
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 0 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [[#289](https://github.com/nf-core/differentialabundance/pull/289)] - Fix missing ch_gene_sets default for gprofiler2 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#299](https://github.com/nf-core/differentialabundance/pull/299)] - Add exclusions for 3.0.1 template update ([@pinin4fjords](https://github.com/pinin4fjords))
 - [[#280](https://github.com/nf-core/differentialabundance/pull/280)] - Bump shinyngs, fix contrasts passed to app creation ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#274](https://github.com/nf-core/differentialabundance/pull/274)] - Fix pagination on samples table ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))

diff --git a/workflows/differentialabundance.nf b/workflows/differentialabundance.nf
@@ -74,6 +74,8 @@ if (run_gene_set_analysis) {
     } else if (params.gprofiler2_run) {
         if (!params.gprofiler2_token && !params.gprofiler2_organism) {
             error("To run gprofiler2, please provide a run token, GMT file or organism!")
+        } else {
+            ch_gene_sets = [[]]     // For gprofiler2 which calls ch_gene_sets.first()
         }
     }
 }