Change the internal type of NextflowAuto.publish to strictly use 'Str…

…ing'

TODO change how the nextflow layer handles the parameter

src/main/scala/io/viash/platforms/nextflow/NextflowAuto.scala

@@ -55,12 +55,8 @@ case class NextflowAuto(
       |Default: `false`.
       |""".stripMargin)
   @default("False")
-  publish: Either[Boolean, String] = Left(false)
+  publish: Either[Boolean, String] = Right("false")
 ) {
-  // if publish is a string, it must be "state"
-  val checkPublish = publish match {
-    case Left(value) => true
-    case Right(value) => value == "state"
-  }
-  assert(checkPublish, message = "publish must be either a boolean or equal to \"state\"")
+  assert(publish.isRight, message = "expected publish to be converted to a string")
+  assert(Seq("true", "false", "state").contains(publish.toOption.get), message = "publish must be either a boolean or equal to \"state\"")
 }

src/main/scala/io/viash/platforms/nextflow/package.scala

@@ -28,7 +28,22 @@ package object nextflow {
   implicit val decodeNextflowDirectives: Decoder[NextflowDirectives] = deriveConfiguredDecoderFullChecks
 
   implicit val encodeNextflowAuto: Encoder.AsObject[NextflowAuto] = deriveConfiguredEncoder
-  implicit val decodeNextflowAuto: Decoder[NextflowAuto] = deriveConfiguredDecoderFullChecks
+  implicit val decodeNextflowAuto: Decoder[NextflowAuto] = deriveConfiguredDecoderFullChecks[NextflowAuto].prepare(
+    _.withFocus(_.mapObject{ conf => 
+      val publish = conf.apply("publish").map {
+        publish => 
+          publish.asBoolean match {
+            case Some(true) => Json.fromString("true")
+            case Some(false) => Json.fromString("false")
+            case None => publish
+          }
+      }
+      publish match {
+        case Some(publish) => conf.add("publish", publish)
+        case None => conf
+      }
+      })
+  )
 
   implicit val encodeNextflowConfig: Encoder.AsObject[NextflowConfig] = deriveConfiguredEncoder
   implicit val decodeNextflowConfig: Decoder[NextflowConfig] = deriveConfiguredDecoderFullChecks