Merge pull request #278 from WackerO/fix_gpro_genesets

Fix gprofiler2 genesets default object

CHANGELOG.md

@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [[#278](https://github.com/nf-core/differentialabundance/pull/278)] - Fix missing ch_gene_sets when running gprofiler without gene sets ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#267](https://github.com/nf-core/differentialabundance/pull/267)] - Whitespace fix, remove TODO, also update changelog for release release 1.5.0 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#265](https://github.com/nf-core/differentialabundance/pull/265)] - GSEA- pngs and htmls in same place ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#257](https://github.com/nf-core/differentialabundance/pull/257)] - Fixed FILTER_DIFFTABLE module, updated PROTEUS module to better handle whitespace in prefix param, made docs clearer ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))

workflows/differentialabundance.nf

@@ -62,6 +62,7 @@ if (params.control_features) { ch_control_features = Channel.of([ exp_meta, file
 def run_gene_set_analysis = params.gsea_run || params.gprofiler2_run
 
 if (run_gene_set_analysis) {
+    ch_gene_sets = Channel.of([])    // For methods that can run without gene sets
     if (params.gene_sets_files) {
         gene_sets_files = params.gene_sets_files.split(",")
         ch_gene_sets = Channel.of(gene_sets_files).map { file(it, checkIfExists: true) }
@@ -74,8 +75,6 @@ if (run_gene_set_analysis) {
         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 methods that can run without gene sets
     }
 }