[Luna] Address PR review comments

- Remove configParams usage, use params directly (contains config defaults)
- Revert getDefaultConfigurations() to original implementation
- Keep only cliParams in getParamsheetConfigurations() for CLI override
- Merge order: params + row + cliParams = config defaults + paramsheet + CLI params

Author: suzannejin

subworkflows/local/utils_nfcore_differentialabundance_pipeline/main.nf

@@ -402,19 +402,15 @@ def getParamsheetConfigurations() {
             // Priority: CLI params (+ params-file) > paramsheet > config defaults
             // Use nextflow session to distinguish CLI params from config defaults
             def cliParams = nextflow.Global.session.cliParams ?: [:]
-            def configParams = nextflow.Global.session.configParams ?: [:]
-            def fullparamset = configParams + row + cliParams
+            def fullparamset = params + row + cliParams
             return fullparamset
         }
 }
 
 // Get default configurations from pipeline parameters
 def getDefaultConfigurations() {
     // replace null by string 'contrasts' for paramset_name to avoid certain problems with null object
-    // Priority: CLI params > defaults
-    def cliParams = nextflow.Global.session.cliParams ?: [:]
-    def configParams = nextflow.Global.session.configParams ?: [:]
-    return [configParams + cliParams + [paramset_name: 'contrasts']]
+    return [params + [paramset_name: 'contrasts']]
 }
 
 // Load configurations from yaml file