Remove preprocessParams from tests

src/main/resources/io/viash/runners/nextflow/channel/channelFromParams.nf

@@ -56,6 +56,12 @@ private List<Tuple2<String, Map<String, Object>>> _paramsToParamSets(Map params,
 
   /* combine arguments into channel */
   /**********************************/
+
+  // Fetch default values for arguments
+  def defaultArgs = config.allArguments
+    .findAll { it.containsKey("default") }
+    .collectEntries { [ it.plainName, it.default ] }
+
   def processedParams = paramSets.indexed().collect{ index, tup ->
     // Process ID
     def id = tup[0] ?: globalID
@@ -67,7 +73,7 @@ private List<Tuple2<String, Map<String, Object>>> _paramsToParamSets(Map params,
     assert id != null: "Each parameter set should have at least an 'id'"
 
     // Process params
-    def parValues = globalParams + tup[1]
+    def parValues = defaultArgs + globalParams + tup[1]
     // // Remove parameters which are null, if the default is also null
     // parValues = parValues.collectEntries{paramName, paramValue ->
     //   parameterSettings = config.functionality.allArguments.find({it.plainName == paramName})

src/test/resources/testnextflowvdsl3/workflows/pipeline3/main.nf

@@ -1,12 +1,11 @@
 nextflow.enable.dsl=2
 
-include { readConfig; helpMessage; preprocessInputs; channelFromParams } from "${params.rootDir}/workflows/utils/WorkflowHelper.nf"
+include { readConfig; helpMessage; channelFromParams } from "${params.rootDir}/workflows/utils/WorkflowHelper.nf"
 config = readConfig("${params.rootDir}/workflows/pipeline3/config.vsh.yaml")
 
 workflow base {
   helpMessage(config)
 
   channelFromParams(params, config)
-    | preprocessInputs(["config": config])
     | view {"DEBUG: $it"}
 }