Fix issue with outputDir and make reamining variables read only

src/main/java/com/askimed/nf/test/lang/TestContext.java

@@ -83,7 +83,7 @@ public WorkflowMeta getWorkflow() {
 	}
 
 	public void setWorkflow(Workflow workflow) {
-		this.workflow = workflow;
+		throw new RuntimeException("Variable 'workflow' is read only");
 	}
 
 	public Snapshot snapshot(Object... object) {
@@ -94,4 +94,35 @@ public void loadParams(String filename) throws CompilationFailedException, Class
 		params.load(filename);
 	}
 
+	public void setOutputDir(String outputDir) {
+		// The 'outputDir' variable is read-only. If an update occurs within the
+		// 'params' closure, update the 'outputDir' key in the hashmap instead of
+		// modifying the variable itself. This fixes issue 125.
+		params.put("outputDir", outputDir);
+	}
+
+	public void setBaseDir(String baseDir) {
+		throw new RuntimeException("Variable 'baseDir' is read only");
+	}
+
+	public void setLaunchDir(String launchDir) {
+		throw new RuntimeException("Variable 'launchDir' is read only");
+	}
+
+	public void setModuleDir(String moduleDir) {
+		throw new RuntimeException("Variable 'moduleDir' is read only");
+	}
+
+	public void setModuleTestDir(String moduleTestDir) {
+		throw new RuntimeException("Variable 'moduleTestDir' is read only");
+	}
+
+	public void setProjectDir(String projectDir) {
+		throw new RuntimeException("Variable 'projectDir' is read only");
+	}
+
+	public void setWorkDir(String workDir) {
+		throw new RuntimeException("Variable 'workDir' is read only");
+	}
+
 }

src/test/java/com/askimed/nf/test/lang/WorkflowTest.java

@@ -124,4 +124,13 @@ public void testWorkflowNonUniqueFilenames() throws Exception {
 
 	}
 
+
+	@Test
+	public void testIssue125() throws Exception {
+
+	  App app = new App();
+	  int exitCode = app.run(new String[] { "test", "test-data/workflow/issue125/example_wf.nf.test"});
+	  assertEquals(0, exitCode);
+
+	}
 }

test-data/workflow/issue125/example_wf.nf

@@ -0,0 +1,36 @@
+process exampleProc {
+
+    storeDir "${outputDir}/exampleProc"
+    input:
+        tuple(
+            val(outputDir),
+            val(localOutputDir),
+        )
+
+    output:
+        tuple(
+            val(outputDir),
+            path("example_output/example*.txt")
+        )
+
+    shell:
+        """
+        mkdir -p !{localOutputDir}
+        touch "!{localOutputDir}/example1.txt"
+        touch "!{localOutputDir}/example2.txt"
+        """
+}
+
+
+workflow PipeWf {
+    take:
+        inputCh
+
+    main:
+        inputCh
+            | exampleProc
+            | set { outputCh }
+
+    emit:
+        outputCh
+}

test-data/workflow/issue125/example_wf.nf.test

@@ -0,0 +1,50 @@
+
+nextflow_workflow {
+
+    name "Test workflow"
+    script "./example_wf.nf"
+    workflow "PipeWf"
+
+    // This example worked correctly in 0.7.3 but fails in 0.8.0
+    test("Output will not exist in default outputDir") {
+
+        when {
+
+            params {
+                outputDir = "$outputDir"
+                localOutputDir = "example_output"
+            }
+            workflow {
+                """
+                input[0] = Channel.of([params.outputDir,params.localOutputDir])
+                """
+            }
+        }
+
+        then {
+              assert workflow.success
+              assert path("${outputDir}/exampleProc/example_output").exists()
+            }
+    }
+
+    test("Output will exist in default outputDir") {
+
+        when {
+
+            params {
+                outDir = "$outputDir"
+                localOutputDir = "example_output"
+            }
+            workflow {
+                """
+                input[0] = Channel.of([params.outDir,params.localOutputDir])
+                """
+            }
+        }
+
+        then {
+              assert workflow.success
+              assert path("${outputDir}/exampleProc/example_output").exists()
+            }
+    }
+}