Nextflow runner: add runElse

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

@@ -27,9 +27,11 @@ def runEach(Map args) {
   def toState_ = args.toState
   def filter_ = args.filter
   def runIf_ = args.runIf
+  def runElse_ = args.runElse
   def id_ = args.id
 
   assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+  assert !runElse_ || runElse_ instanceof Closure: "runElse: must pass a Closure to runElse."
 
   workflow runEachWf {
     take: input_ch
@@ -65,6 +67,15 @@ def runEach(Map args) {
         chRun = id_ch
         chPassthrough = Channel.empty()
       }
+      def chPassthroughElse = null
+      if (runElse_){
+        chPassthroughElse = chPassthrough.map{tup ->
+          runElse_(tup[0], tup[1], comp_)
+        }
+      } else {
+       chPassthroughElse = Channel.empty() 
+      }
+
       def data_ch = chRun | map{tup ->
           def new_data = tup[1]
           if (fromState_ instanceof Map) {
@@ -105,7 +116,7 @@ def runEach(Map args) {
         : out_ch
 
       def return_ch = post_ch
-        | concat(chPassthrough)
+        | concat(chPassthroughElse)
 
       return_ch
     }

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

@@ -14,7 +14,7 @@ def processWorkflowArgs(Map args, Map defaultWfArgs, Map meta) {
   assert key ==~ /^[a-zA-Z_]\w*$/ : "Error in module '$key': Expected process argument 'key' to consist of only letters, digits or underscores. Found: ${key}"
 
   // check for any unexpected keys
-  def expectedKeys = ["key", "directives", "auto", "map", "mapId", "mapData", "mapPassthrough", "filter", "runIf", "fromState", "toState", "args", "renameKeys", "debug"]
+  def expectedKeys = ["key", "directives", "auto", "map", "mapId", "mapData", "mapPassthrough", "filter", "runIf", "runElse", "fromState", "toState", "args", "renameKeys", "debug"]
   def unexpectedKeys = workflowArgs.keySet() - expectedKeys
   assert unexpectedKeys.isEmpty() : "Error in module '$key': unexpected arguments to the '.run()' function: '${unexpectedKeys.join("', '")}'"
 

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

@@ -118,6 +118,15 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       chPassthrough = Channel.empty()
     }
 
+    def chPassthroughElse = null
+    if (workflowArgs.runElse_){
+      chPassthroughElse = chPassthrough.map{tup ->
+        workflowArgs.runElse_(tup[0], tup[1])
+      }
+    } else {
+      chPassthroughElse = Channel.empty() 
+    }
+
     def chRunFiltered = workflowArgs.filter ?
       chRun | filter{workflowArgs.filter(it)} :
       chRun

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

@@ -12,7 +12,8 @@ workflow base {
   ])
     | step1.run(
       filter: { id, data -> id != "three" },
-      runIf: { id, data -> data.input.size() == 2 || id == "three" }
+      runIf: { id, data -> data.input.size() == 2 || id == "three" },
+      runElse: {it}
     )
     | view{"output: $it"}
     | toSortedList{ a, b -> a[0] <=> b[0] }