Fix using .run() without fromState defined an an input channel of t…

…uples with more than two elements. (#587)

* Add failing example

* Implement fix

* Add CHANGELOG entry

CHANGELOG.md

@@ -27,7 +27,15 @@ TODO add summary
 ## BUG FIXES
 
 * `__merge__`: Handle invalid yaml during merging (PR #570). There was not enough error handling during this operation. Switched to the more advanced `Convert.textToJson` helper method.
-
+
+
+
+
+
+## BUG FIXES
+
+* `NextflowPlatform`: Fix `Invalid method invocation 'call'` error when using `.run()` without `fromState` defined and the input channel holds tuples with more than two elements (PR #587). This issue also impacts some other helper functionality like `runEach()`. 
+
 # Viash 0.8.0 (2023-10-23): Nextflow workflows and dependencies
 
 Nextflow workflows definitions are picked up by Viash and assembled into a functional Nextflow workflow, reducing the amount of boilerplate code needed to be written by the user.

src/main/resources/io/viash/runners/nextflow/workflowFactory/workflowFactory.nf

@@ -120,7 +120,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         def new_data = workflowArgs.fromState(it.take(2))
         [it[0], new_data]
       } :
-      chRun
+      chRun | map {tup -> tup.take(2)}
 
     // fill in defaults
     chArgsWithDefaults = chArgs

src/test/resources/testnextflowvdsl3/src/test_wfs/nested/main.nf

@@ -9,10 +9,9 @@ workflow base {
       file = tempFile()
       file.write("num: $num")
 
-      ["num$num", [ num: num, file: file ]]
+      ["num$num", [ file: file ], ["num": num]]
     }
     | sub_workflow.run(
-      fromState: ["file": "file"],
       toState: {id, output, state -> 
         def newState = [
           "step1_output": output.output, 
@@ -22,8 +21,8 @@ workflow base {
         return newState
       }
     )
-    | view{ id, state ->
-      def num = state.num
+    | view{ id, state, extra ->
+      def num = extra.num
 
       // check id
       assert id == "num$num": "id should be 'num$num'. Found: '$id'"