Nextflow parameter check

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

@@ -33,11 +33,32 @@ private List<Tuple2<String, Map<String, Object>>> _paramsToParamSets(Map params,
   // todo: fetch key from run args
   def key_ = config.name
 
+  def allowedExtra = [
+    "override_container_registry",
+    "publishDir",
+    "publish-dir",
+    "publish_dir",
+    "transcripts-dir",
+    "transcriptsDir",
+    "param_list",
+    "id"
+  ]
   /* parse regular parameters (not in param_list)  */
   /*************************************************/
   def globalParams = config.allArguments
     .findAll { params.containsKey(it.plainName) }
     .collectEntries { [ it.plainName, params[it.plainName] ] }
+  // Get the non-overwrite params. This could result in false negatives:
+  // these arguments are not checked for validity.
+  // Note that overrides can only be set in `params` and not through an
+  // entry in param_list.
+  def nonOverwriteParams = params.findAll{k, v -> !k.contains("__")}
+  // When the parameter name is formatted using camelCase,
+  // a second parameter is created with the same value using
+  // kebab-case, and vice versa.
+  def configParamNames = config.allArguments.collect{it.plainName}
+  def leftover = nonOverwriteParams.keySet().collect() - configParamNames - allowedExtra
+  assert leftover.isEmpty(): "Found invalid parameter(s) for ${key_}: ${leftover}"
   def globalID = params.get("id", null)
 
   /* process params_list arguments */
@@ -66,6 +87,9 @@ private List<Tuple2<String, Map<String, Object>>> _paramsToParamSets(Map params,
     }
     assert id != null: "Each parameter set should have at least an 'id'"
 
+    def extraArgs = tup[1].keySet().collect() - ["id"] - configParamNames
+    assert extraArgs.isEmpty(): "Found invalid parameter(s) in param_list, id ${id}: ${extraArgs}"
+
     // Process params
     def parValues = globalParams + tup[1]
     // // Remove parameters which are null, if the default is also null

src/test/scala/io/viash/runners/nextflow/NextflowScriptTest.scala

@@ -67,6 +67,22 @@ class NextflowScriptTest extends AnyFunSuite with BeforeAndAfterAll {
     assert(exitCode == 0, s"\nexit code was $exitCode\nStd output:\n$stdOut\nStd error:\n$stdErr")
   }
 
+  test("Test nonexistant parameter fails", NextflowTest) {
+    val (exitCode, stdOut, stdErr) = NextflowTestHelper.run(
+      mainScript = "target/nextflow/wf/main.nf",
+      args = List(
+        "--id", "foo",
+        "--input1", "resources/lines*.txt",
+        "--input2", "resources/lines3.txt",
+        "--publish_dir", "output",
+        "--nonexistant", "bar",
+      ),
+      cwd = tempFolFile
+    )
+    assert(stdOut.contains("Found invalid parameter(s) for"))
+    assert(exitCode == 1, s"\nexit code was $exitCode\nStd output:\n$stdOut\nStd error:\n$stdErr")
+  }
+
   test("Run config pipeline with symlink", NextflowTest) {
     val newWorkflowPath = Paths.get(tempFolStr, "workflowsAsSymlink")
     Files.createDirectories(newWorkflowPath)

src/test/scala/io/viash/runners/nextflow/WorkflowHelperTest.scala

@@ -130,6 +130,32 @@ class WorkflowHelperTest extends AnyFunSuite with BeforeAndAfterAll {
     )
   }
 
+  test("Run config pipeline with yamlblob and invalid parameter", NextflowTest) {
+    val fooArgs =
+      "{id: foo, input: resources/lines3.txt, whole_number: 3, optional_with_default: foo, multiple: [a, b, c], doesnotexist: lorem}"
+    val barArgs =
+      "{id: bar, input: resources/lines5.txt, real_number: 0.5, optional: bar, reality: true}"
+
+    val (exitCode, stdOut, stdErr) = NextflowTestHelper.run(
+      mainScript = "workflows/pipeline3/main.nf",
+      entry = Some("base"),
+      args = List(
+        "--param_list", s"[$fooArgs, $barArgs]",
+        "--real_number", "10.5",
+        "--whole_number", "10",
+        "--str", "foo",
+        "--publish_dir", "output",
+      ),
+      cwd = tempFolFile
+    )
+    assert(stdOut.contains("Found invalid parameter(s) for"))
+    assert(
+      exitCode == 1,
+      s"\nexit code was $exitCode\nStd output:\n$stdOut\nStd error:\n$stdErr"
+    )
+
+  }
+
   test("Run config pipeline with yaml file", NextflowTest) {
     val param_list_file =
       Paths.get(resourcesPath, "pipeline3.yaml").toFile.toString