Fix params block in included module (#6940)

Co-authored-by: Jorge Ejarque <jorgee@users.noreply.github.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>

Author: bentsherman

modules/nextflow/src/main/groovy/nextflow/Session.groovy

@@ -1094,7 +1094,6 @@ class Session implements ISession {
     }
 
     void notifyAfterWorkflowExecution() {
-
     }
 
     void notifyFlowBegin() {

modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy

@@ -44,9 +44,11 @@ abstract class BaseScript extends Script implements ExecutionContext {
 
     private ScriptMeta meta
 
+    private ParamsDef paramsDef
+
     private WorkflowDef entryFlow
 
-    private OutputDef publisher
+    private OutputDef outputDef
 
     @Lazy InputStream stdin = { System.in }()
 
@@ -113,13 +115,7 @@ abstract class BaseScript extends Script implements ExecutionContext {
         if( ExecutionStack.withinWorkflow() )
             throw new IllegalStateException("Workflow params definition is not allowed within a workflow")
 
-        final dsl = new ParamsDsl()
-        final cl = (Closure)body.clone()
-        cl.setDelegate(dsl)
-        cl.setResolveStrategy(Closure.DELEGATE_FIRST)
-        cl.call()
-
-        dsl.apply(session)
+        this.paramsDef = new ParamsDef(body)
     }
 
     /**
@@ -182,21 +178,21 @@ abstract class BaseScript extends Script implements ExecutionContext {
     /**
      * Define an output block.
      *
-     * @param closure
+     * @param body
      */
-    protected void output(Closure closure) {
+    protected void output(Closure body) {
         if( !entryFlow )
             throw new IllegalStateException("Workflow output definition must be defined after the entry workflow")
         if( ExecutionStack.withinWorkflow() )
             throw new IllegalStateException("Workflow output definition is not allowed within a workflow")
 
-        publisher = new OutputDef(closure)
+        this.outputDef = new OutputDef(body)
     }
 
     protected IncludeDef include( IncludeDef include ) {
-        if(ExecutionStack.withinWorkflow())
+        if( ExecutionStack.withinWorkflow() )
             throw new IllegalStateException("Include statement is not allowed within a workflow definition")
-        include .setSession(session)
+        return include.setSession(session)
     }
 
     /**
@@ -246,9 +242,11 @@ abstract class BaseScript extends Script implements ExecutionContext {
 
         // invoke the entry workflow
         session.notifyBeforeWorkflowExecution()
+        if( paramsDef )
+            paramsDef.apply(session)
         final ret = entryFlow.invoke_a(BaseScriptConsts.EMPTY_ARGS)
-        if( publisher )
-            publisher.apply(session)
+        if( outputDef )
+            outputDef.apply(session)
         session.notifyAfterWorkflowExecution()
         return ret
     }

modules/nextflow/src/main/groovy/nextflow/script/BaseScriptConsts.groovy

@@ -25,5 +25,5 @@ class BaseScriptConsts {
 
     public static Object[] EMPTY_ARGS = [] as Object[]
 
-    public static List<String> PRIVATE_NAMES = ['session','processFactory','taskProcessor','meta','entryFlow', 'publisher']
+    public static List<String> PRIVATE_NAMES = ['session', 'processFactory', 'taskProcessor', 'meta', 'paramsDef', 'entryFlow', 'outputDef']
 }

modules/nextflow/src/main/groovy/nextflow/script/OutputDef.groovy

@@ -18,7 +18,6 @@ package nextflow.script
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-import groovyx.gpars.dataflow.DataflowWriteChannel
 import nextflow.Session
 /**
  * Models the workflow output definition

modules/nextflow/src/main/groovy/nextflow/script/ParamsDef.groovy

@@ -0,0 +1,45 @@
+/*
+ * Copyright 2013-2026, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package nextflow.script
+
+import groovy.transform.CompileStatic
+import nextflow.Session
+/**
+ * Models the workflow params definition
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+@CompileStatic
+class ParamsDef {
+
+    private Closure closure
+
+    ParamsDef(Closure closure) {
+        this.closure = closure
+    }
+
+    void apply(Session session) {
+        final dsl = new ParamsDsl()
+        final cl = (Closure)closure.clone()
+        cl.setDelegate(dsl)
+        cl.setResolveStrategy(Closure.DELEGATE_FIRST)
+        cl.call()
+
+        dsl.apply(session)
+    }
+
+}