diff --git a/CHANGELOG.md b/CHANGELOG.md
index 983bad0af..2e89bd247 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,12 @@ TODO add summary
 * `export json_schema`: Add a `--strict` option to output a subset of the schema representing the internal structure of the Viash config (PR #564).
 
 * `config view` and `ns list`: Do not output internal functionality fields (#564). Additionally, add a validation that no internal fields are present when reading a Viash config file.
+
+## MINOR CHANGES
+
+* `testbenches`: Add testbenches for local dependencies (PR #565).
+
+* `testbenches`: Refactor testbenches helper functions to uniformize them (PR #565).
   
 # Viash 0.8.0-RC5 (2023-10-11): Fix run workflow
 
diff --git a/src/test/scala/io/viash/TestHelper.scala b/src/test/scala/io/viash/TestHelper.scala
index b92d11cd5..4224a6669 100644
--- a/src/test/scala/io/viash/TestHelper.scala
+++ b/src/test/scala/io/viash/TestHelper.scala
@@ -10,94 +10,65 @@ import scala.reflect.ClassTag
 
 object TestHelper {
 
-  case class ExceptionOutput(
-    exceptionText: String,
-    output: String,
-    error: String,
+  case class TestMainOutput(
+    stdout: String,
+    stderr: String,
+    exitCode: Option[Int],
+    exceptionText: Option[String],
   )
 
   /**
-   * Method to capture the console stdout generated by Main.main() so we can analyse what's being outputted to the console
-   * As the capture prevents the stdout being printed to the console, we print it after the Main.main() is finished.
+   * Method to capture the console stdout and stderr generated by Main.main() so we can analyse what's being outputted to the console
    * @param args all the arguments typically passed to Main.main()
-   * @return a string of all the output
+   * @return TestMainOutput containing the console output text and exit code
    */
-  def testMain(args: String*) : String = {
-    val os = new ByteArrayOutputStream()
-    Console.withErr(os) {
-      Console.withOut(os) {
-        Main.mainCLI(args.toArray)
-      }
-    }
-
-    val stdout = os.toString
-    // Console.print(stdout)
-    stdout
-  }
+  def testMain(args: String*): TestMainOutput = testMain(None, args: _*)
 
   /**
    * Method to capture the console stdout and stderr generated by Main.main() so we can analyse what's being outputted to the console
-   * As the capture prevents the stdout and stderr being printed to the console, we print it after the Main.main() is finished.
+   * @param workingDir the working directory to run the command in
    * @param args all the arguments typically passed to Main.main()
-   * @return a tuple of stdout and stderr strings of all the output
+   * @return TestMainOutput containing the console output text and exit code
    */
-  def testMainWithStdErr(args: String*) : (String, String, Int) = {
+  def testMain(workingDir: Option[Path], args: String*): TestMainOutput = {
     val outStream = new ByteArrayOutputStream()
     val errStream = new ByteArrayOutputStream()
     val exitCode = Console.withOut(outStream) {
       Console.withErr(errStream) {
-        Main.mainCLI(args.toArray)
+        Main.mainCLI(args.toArray, workingDir)
       }
     }
 
-    val stdout = outStream.toString
-    val stderr = errStream.toString
-    // Console.print(stdout)
-    (stdout, stderr, exitCode)
+    TestMainOutput(outStream.toString, errStream.toString, Some(exitCode), None)
   }
 
   /**
-   * Method to capture the console stdout generated by Main.main() so we can analyse what's being outputted to the console
-   * As the capture prevents the stdout being printed to the console, we print it after the Main.main() is finished.
-   * Additionally it handles a thrown RuntimeException using assertThrows
+   * Method to capture the console stdout and stderr generated by Main.main() so we can analyse what's being outputted to the console.
+   * Additionally it handles a thrown Exception/Throwable and returns the exception text.
    * @param args all the arguments typically passed to Main.main()
-   * @return a string of all the output
+   * @return TestMainOutput containing the exception text and the console output text
    */
-  def testMainException[T <: AnyRef: ClassTag](args: String*) : String = {
-    val os = new ByteArrayOutputStream()
-    assertThrows[T] {
-      Console.withOut(os) {
-        Main.mainCLI(args.toArray)
-      }
-    }
-
-    val stdout = os.toString
-    // Console.print(stdout)
-    stdout
-  }
+  def testMainException[T <: Throwable](args: String*)(implicit classTag: ClassTag[T]) : TestMainOutput = testMainException(None, args: _*)
 
   /**
-   * Method to capture the console stdout generated by Main.main() so we can analyse what's being outputted to the console
-   * As the capture prevents the stdout being printed to the console, we print it after the Main.main() is finished.
-   * Additionally it handles a thrown RuntimeException using assertThrows
+   * Method to capture the console stdout and stderr generated by Main.main() so we can analyse what's being outputted to the console.
+   * Additionally it handles a thrown Exception/Throwable and returns the exception text.
+   * @param workingDir the working directory to run the command in
    * @param args all the arguments typically passed to Main.main()
-   * @return ExceptionOutput containing the exception text and the console output text
+   * @return TestMainOutput containing the exception text and the console output text
    */
-  def testMainException2[T <: Exception](args: String*) : ExceptionOutput = {
+  def testMainException[T <: Throwable](workingDir: Option[Path], args: String*)(implicit classTag: ClassTag[T]) : TestMainOutput = {
     val outStream = new ByteArrayOutputStream()
     val errStream = new ByteArrayOutputStream()
-    val caught = intercept[Exception] {
+    val caught = intercept[T] {
       Console.withOut(outStream) {
         Console.withErr(errStream) {
-          Main.mainCLI(args.toArray)
+          Main.mainCLI(args.toArray, workingDir)
         }
       }
     }
 
-    val stdout = outStream.toString
-    val stderr = errStream.toString
-    // Console.print(stdout)
-    ExceptionOutput(caught.getMessage, stdout, stderr)
+    TestMainOutput(outStream.toString, errStream.toString, None, Some(caught.getMessage))
   }
 
 
diff --git a/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerChown.scala b/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerChown.scala
index 426206efc..73749d4f8 100644
--- a/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerChown.scala
+++ b/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerChown.scala
@@ -116,13 +116,13 @@ class MainBuildAuxiliaryDockerChown extends AnyFunSuite with BeforeAndAfterAll w
   test("Test with platform and chown is set to false", DockerTest) {
     val newConfigFile = configDeriver.derive(""".platforms := [{type: "docker", chown: false }]""", "docker_chown_false")
     // functionality not provided in runner, should throw exception
-    val output = TestHelper.testMainException2[ConfigParserException](
+    val output = TestHelper.testMainException[ConfigParserException](
       "build",
       "--engine", "docker_chown",
       "-o", tempFolStr,
       newConfigFile
     )
-    assert(output.error.contains("Error: ..chown was removed: Compability not provided with the Runners functionality."))
+    assert(output.stderr.contains("Error: ..chown was removed: Compability not provided with the Runners functionality."))
   }
 
   override def afterAll(): Unit = {
diff --git a/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerRequirements.scala b/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerRequirements.scala
index c7d16867d..3242a4d4d 100644
--- a/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerRequirements.scala
+++ b/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerRequirements.scala
@@ -568,29 +568,29 @@ class MainBuildAuxiliaryDockerRequirementsApkTest extends AbstractMainBuildAuxil
   test("test_setup; check the fortune package is added for the test option", DockerTest) { f =>
     val newConfigFilePath = deriveEngineConfig(None, Some("""[{ "type": "apk", "packages": ["fortune"] }]"""), "apk_test_fortune_test")
 
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       newConfigFilePath
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 1 out of 1 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 1 out of 1 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
   }
 
   test("test_setup; check the fortune package is not added for the test option when not specified", DockerTest) { f =>
     val newConfigFilePath = deriveEngineConfig(None, None, "apk_base_test")
 
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "test",
       "-k", "false",
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText == "Only 0 out of 1 test scripts succeeded!")
+    assert(testOutput.exceptionText.get == "Only 0 out of 1 test scripts succeeded!")
 
-    assert(testOutput.output.contains("Running tests in temporary directory: "))
-    assert(testOutput.output.contains("ERROR! Only 0 out of 1 test scripts succeeded!"))
-    assert(testOutput.output.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("ERROR! Only 0 out of 1 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
   }
 }
diff --git a/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerResourceCopying.scala b/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerResourceCopying.scala
index ff17f663e..98690930c 100644
--- a/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerResourceCopying.scala
+++ b/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerResourceCopying.scala
@@ -77,14 +77,14 @@ class MainBuildAuxiliaryDockerResourceCopying extends AnyFunSuite with BeforeAnd
   test("Check resources with unsupported format") {
     val configResourcesUnsupportedProtocolFile = configDeriver.derive(""".functionality.resources := [{type: "bash_script", path: "./check_bash_version.sh"}, {path: "ftp://ftp.ubuntu.com/releases/robots.txt"}]""", "config_resource_unsupported_protocol").toString
     // generate viash script
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "build",
       "--engine", "docker",
       "-o", tempFolStr,
       configResourcesUnsupportedProtocolFile
     )
 
-    assert(testOutput.exceptionText == "Unsupported scheme: ftp")
+    assert(testOutput.exceptionText.get == "Unsupported scheme: ftp")
   }
 
   override def afterAll(): Unit = {
diff --git a/src/test/scala/io/viash/auxiliary/MainTestAuxiliaryDockerResourceCopy.scala b/src/test/scala/io/viash/auxiliary/MainTestAuxiliaryDockerResourceCopy.scala
index d968c251a..e9e6228ef 100644
--- a/src/test/scala/io/viash/auxiliary/MainTestAuxiliaryDockerResourceCopy.scala
+++ b/src/test/scala/io/viash/auxiliary/MainTestAuxiliaryDockerResourceCopy.scala
@@ -29,7 +29,7 @@ class MainTestAuxiliaryDockerResourceCopy extends AnyFunSuite with BeforeAndAfte
     Files.copy(tmpFolderResourceSourceFile, tmpFolderResourceDestinationFile, StandardCopyOption.REPLACE_EXISTING)
 
     // generate viash script
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "docker",
       "-k", "true",
@@ -37,13 +37,13 @@ class MainTestAuxiliaryDockerResourceCopy extends AnyFunSuite with BeforeAndAfte
     )
 
     // basic checks to see if standard test/build was correct
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("WARNING! No tests found!"))
-    assert(!testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("WARNING! No tests found!"))
+    assert(!testOutput.stdout.contains("Cleaning up temporary directory"))
 
     val FolderRegex = ".*Running tests in temporary directory: '([^']*)'.*".r
 
-    val tempPath = testText.replaceAll("\n", "") match {
+    val tempPath = testOutput.stdout.replaceAll("\n", "") match {
       case FolderRegex(path) => path
       case _ => ""
     }
@@ -77,27 +77,27 @@ class MainTestAuxiliaryDockerResourceCopy extends AnyFunSuite with BeforeAndAfte
     }
 
     Directory(tmpFolderResourceDestinationFolder).deleteRecursively()
-    checkTempDirAndRemove(testText, true, "viash_test_auxiliary_resources")
+    checkTempDirAndRemove(testOutput.stdout, true, "viash_test_auxiliary_resources")
   }
 
   test("Check resources with unsupported format", DockerTest) {
     val configResourcesUnsupportedProtocolFile = configDeriver.derive(""".functionality.resources := [{type: "bash_script", path: "./check_bash_version.sh"}, {path: "ftp://ftp.ubuntu.com/releases/robots.txt"}]""", "config_resource_unsupported_protocol").toString
     // generate viash script
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "test",
       "--engine", "docker",
       "-k", "true",
       configResourcesUnsupportedProtocolFile
     )
 
-    assert(testOutput.exceptionText == "Unsupported scheme: ftp")
+    assert(testOutput.exceptionText.get == "Unsupported scheme: ftp")
 
     // basic checks to see if standard test/build was correct
-    assert(testOutput.output.contains("Running tests in temporary directory: "))
-    assert(!testOutput.output.contains("WARNING! No tests found!"))
-    assert(!testOutput.output.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(!testOutput.stdout.contains("WARNING! No tests found!"))
+    assert(!testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testOutput.output, true, "viash_test_auxiliary_resources")
+    checkTempDirAndRemove(testOutput.stdout, true, "viash_test_auxiliary_resources")
   }
 
   /**
diff --git a/src/test/scala/io/viash/e2e/build/DockerMoreSuite.scala b/src/test/scala/io/viash/e2e/build/DockerMoreSuite.scala
index ff9e505cd..de40089fa 100644
--- a/src/test/scala/io/viash/e2e/build/DockerMoreSuite.scala
+++ b/src/test/scala/io/viash/e2e/build/DockerMoreSuite.scala
@@ -36,7 +36,7 @@ class DockerMoreSuite extends AnyFunSuite with BeforeAndAfterAll {
       "commands_default"
     )
     
-    val (stdout, _, _) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "build",
       "--engine", "docker",
       "--runner", "docker",
@@ -45,7 +45,7 @@ class DockerMoreSuite extends AnyFunSuite with BeforeAndAfterAll {
       "--setup", "alwaysbuild"
     )
 
-    assert(stdout.matches("\\[notice\\] Building container 'testbash:0\\.1' with Dockerfile\\s*"), stdout)
+    assert(testOutput.stdout.matches("\\[notice\\] Building container 'testbash:0\\.1' with Dockerfile\\s*"), testOutput.stdout)
   }
 
   test("Verify adding extra commands to verify", DockerTest) {
@@ -54,7 +54,7 @@ class DockerMoreSuite extends AnyFunSuite with BeforeAndAfterAll {
       "commands_extra"
     )
     
-    val (stdout, _, _) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "build",
       "--engine", "docker",
       "--runner", "docker",
@@ -63,7 +63,7 @@ class DockerMoreSuite extends AnyFunSuite with BeforeAndAfterAll {
       "--setup", "alwaysbuild"
     )
 
-    assert(stdout.matches("\\[notice\\] Building container 'testbash:0\\.1' with Dockerfile\\s*"), stdout)
+    assert(testOutput.stdout.matches("\\[notice\\] Building container 'testbash:0\\.1' with Dockerfile\\s*"), testOutput.stdout)
   }
 
   test("Verify base adding an extra required command that doesn't exist", DockerTest) {
@@ -72,7 +72,7 @@ class DockerMoreSuite extends AnyFunSuite with BeforeAndAfterAll {
       "non_existing_command"
     )
     
-    val stdout = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "build",
       "--engine", "docker",
       "--runner", "docker",
@@ -81,14 +81,14 @@ class DockerMoreSuite extends AnyFunSuite with BeforeAndAfterAll {
       "--setup", "alwaysbuild"
     )
 
-    assert(stdout.contains("[notice] Building container 'testbash:0.1' with Dockerfile"))
-    assert(stdout.contains("[error] Docker container 'testbash:0.1' does not contain command 'non_existing_command'."))
+    assert(testOutput.stdout.contains("[notice] Building container 'testbash:0.1' with Dockerfile"))
+    assert(testOutput.stdout.contains("[error] Docker container 'testbash:0.1' does not contain command 'non_existing_command'."))
   }
 
   test("Check deprecated warning", DockerTest) {
     val newConfigFilePath = configDeriver.derive(""".functionality.status := "deprecated"""", "deprecated")
     
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "build",
       "--engine", "docker",
       "--runner", "docker",
@@ -97,8 +97,8 @@ class DockerMoreSuite extends AnyFunSuite with BeforeAndAfterAll {
       "--setup", "alwaysbuild"
     )
 
-    assert(stderr.contains("The status of the component 'testbash' is set to deprecated."))
-    assert(exitCode == 0)
+    assert(testOutput.stderr.contains("The status of the component 'testbash' is set to deprecated."))
+    assert(testOutput.exitCode == Some(0))
   }
 
   test("Check component works when multiple_sep is set to ;", DockerTest) {
@@ -107,7 +107,7 @@ class DockerMoreSuite extends AnyFunSuite with BeforeAndAfterAll {
       "multiple_sep"
     )
     
-    val _ = TestHelper.testMainWithStdErr(
+    val _ = TestHelper.testMain(
       "build",
       "--engine", "docker",
       "--runner", "docker",
diff --git a/src/test/scala/io/viash/e2e/build/NativeSuite.scala b/src/test/scala/io/viash/e2e/build/NativeSuite.scala
index c0521919b..bc0e34d9a 100644
--- a/src/test/scala/io/viash/e2e/build/NativeSuite.scala
+++ b/src/test/scala/io/viash/e2e/build/NativeSuite.scala
@@ -10,6 +10,7 @@ import io.viash.config.Config
 
 import scala.io.Source
 import io.viash.helpers.{IO, Exec, Logger}
+import io.viash.exceptions.ConfigParserException
 
 class NativeSuite extends AnyFunSuite with BeforeAndAfterAll {
   Logger.UseColorOverride.value = Some(false)
@@ -222,11 +223,11 @@ class NativeSuite extends AnyFunSuite with BeforeAndAfterAll {
     )
 
     val testRegex = "Warning: ..platforms is deprecated: Use 'engines' and 'runners' instead.".r
-    assert(testRegex.findFirstIn(testOutput).isDefined, testOutput)
+    assert(testRegex.findFirstIn(testOutput.stderr).isDefined, testOutput)
   }
 
   test("Test whether defining strings as arguments in argument groups throws a removed error") {
-    val testOutput = TestHelper.testMainException2[Exception](
+    val testOutput = TestHelper.testMainException[Exception](
       "build",
       "-o", tempFolStr,
       configDeprecatedArgumentGroups
@@ -241,19 +242,19 @@ class NativeSuite extends AnyFunSuite with BeforeAndAfterAll {
     assert(out.exitValue == 0)
 
     val testRegex = "Error: specifying strings in the .argument field of argument group 'First group' was removed.".r
-    assert(testRegex.findFirstIn(testOutput.error).isDefined, testOutput.error)
+    assert(testRegex.findFirstIn(testOutput.stderr).isDefined, testOutput.stderr)
   }
 
   test("Test whether setting an internalFunctionality field throws an error") {
     val newConfigFilePath = configDeriver.derive(""".functionality.argument_groups[.name == "First group"].arguments[.name == "input"].dest := "foo"""", "set_internal_functionality")
 
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[ConfigParserException](
       "build",
       "-o", tempFolStr,
       newConfigFilePath
     )
 
-    assert(testOutput.error.contains("Error: .functionality.argument_groups.arguments.dest is internal functionality."))
+    assert(testOutput.stderr.contains("Error: .functionality.argument_groups.arguments.dest is internal functionality."))
   }
 
   test("Test config without a main script") {
@@ -264,7 +265,7 @@ class NativeSuite extends AnyFunSuite with BeforeAndAfterAll {
       "-c", ".functionality.resources := []"
     )
 
-    assert(testOutput.contains("Warning: no resources specified!"))
+    assert(testOutput.stderr.contains("Warning: no resources specified!"))
   }
 
   override def afterAll(): Unit = {
diff --git a/src/test/scala/io/viash/e2e/config_view/MainConfigViewSuite.scala b/src/test/scala/io/viash/e2e/config_view/MainConfigViewSuite.scala
index ba31035c0..65a1d4a83 100644
--- a/src/test/scala/io/viash/e2e/config_view/MainConfigViewSuite.scala
+++ b/src/test/scala/io/viash/e2e/config_view/MainConfigViewSuite.scala
@@ -13,23 +13,23 @@ class MainConfigViewSuite extends AnyFunSuite{
 
 
   test("viash config view local") {
-    val (stdout, _, _) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "config", "view",
       configFile
     )
 
-    assert(stdout.startsWith("functionality:"))
-    assert(stdout.contains("testbash"))
+    assert(testOutput.stdout.startsWith("functionality:"))
+    assert(testOutput.stdout.contains("testbash"))
   }
 
   test("viash config view remote") {
-    val (stdout, _, _) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "config", "view",
       "https://raw.githubusercontent.com/viash-io/viash/develop/src/test/resources/testbash/config.vsh.yaml"
     )
 
-    assert(stdout.startsWith("functionality:"))
-    assert(stdout.contains("testbash"))
+    assert(testOutput.stdout.startsWith("functionality:"))
+    assert(testOutput.stdout.contains("testbash"))
   }
 
 }
diff --git a/src/test/scala/io/viash/e2e/export/MainExportSuite.scala b/src/test/scala/io/viash/e2e/export/MainExportSuite.scala
index 04f073df8..fb1ffedca 100644
--- a/src/test/scala/io/viash/e2e/export/MainExportSuite.scala
+++ b/src/test/scala/io/viash/e2e/export/MainExportSuite.scala
@@ -23,15 +23,15 @@ class MainExportSuite extends AnyFunSuite with BeforeAndAfter {
   // These are all *very* basic tests. Practicly no validation whatsoever to check whether the output is correct or not.
 
   test("viash export resource") {
-    val stdout = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "export", "resource", "runners/nextflow/WorkflowHelper.nf"
     )
 
-    assert(stdout.contains("def readConfig("))
+    assert(testOutput.stdout.contains("def readConfig("))
   }
 
   test("viash export resource to file") {
-    val stdout = TestHelper.testMain(
+    TestHelper.testMain(
       "export", "resource", "runners/nextflow/WorkflowHelper.nf",
       "--output", tempFile.toString
     )
@@ -41,38 +41,38 @@ class MainExportSuite extends AnyFunSuite with BeforeAndAfter {
   }
 
   test("viash export resource legacy") {
-    val (stdout, stderr, code) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "export", "resource", "platforms/nextflow/WorkflowHelper.nf"
     )
 
-    assert(stderr.contains("WARNING: The 'platforms/' prefix is deprecated. Please use 'runners/' instead."))
+    assert(testOutput.stderr.contains("WARNING: The 'platforms/' prefix is deprecated. Please use 'runners/' instead."))
 
-    assert(stdout.contains("def readConfig("))
+    assert(testOutput.stdout.contains("def readConfig("))
   }
 
   test("viash export resource to file legacy") {
-    val (stdout, stderr, code) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "export", "resource", "platforms/nextflow/WorkflowHelper.nf",
       "--output", tempFile.toString
     )
 
-    assert(stderr.contains("WARNING: The 'platforms/' prefix is deprecated. Please use 'runners/' instead."))
+    assert(testOutput.stderr.contains("WARNING: The 'platforms/' prefix is deprecated. Please use 'runners/' instead."))
 
     val lines = helpers.IO.read(tempFile.toUri())
     assert(lines.contains("def readConfig("))
   }
   
   test("viash export cli_schema") {
-    val stdout = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "export", "cli_schema"
     )
 
-    assert(stdout.startsWith("""- name: "run""""))
-    assert(stdout.contains("viash config inject"))
+    assert(testOutput.stdout.startsWith("""- name: "run""""))
+    assert(testOutput.stdout.contains("viash config inject"))
   }
   
   test("viash export cli_schema to file") {
-    val stdout = TestHelper.testMain(
+    TestHelper.testMain(
       "export", "cli_schema",
       "--output", tempFile.toString
     )
@@ -83,16 +83,16 @@ class MainExportSuite extends AnyFunSuite with BeforeAndAfter {
   }
 
   test("viash export cli_autocomplete without format") {
-    val stdout = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "export", "cli_autocomplete"
     )
 
-    assert(stdout.startsWith("""# bash completion for viash"""))
-    assert(stdout.contains("COMPREPLY=($(compgen -W 'run build test ns config' -- \"$cur\"))"))
+    assert(testOutput.stdout.startsWith("""# bash completion for viash"""))
+    assert(testOutput.stdout.contains("COMPREPLY=($(compgen -W 'run build test ns config' -- \"$cur\"))"))
   }
 
   test("viash export cli_autocomplete without format to file") {
-    val stdout = TestHelper.testMain(
+    TestHelper.testMain(
       "export", "cli_autocomplete",
       "--output", tempFile.toString
     )
@@ -103,17 +103,17 @@ class MainExportSuite extends AnyFunSuite with BeforeAndAfter {
   }
 
   test("viash export cli_autocomplete Bash") {
-    val stdout = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "export", "cli_autocomplete",
       "--format", "bash"
     )
 
-    assert(stdout.startsWith("""# bash completion for viash"""))
-    assert(stdout.contains("COMPREPLY=($(compgen -W 'run build test ns config' -- \"$cur\"))"))
+    assert(testOutput.stdout.startsWith("""# bash completion for viash"""))
+    assert(testOutput.stdout.contains("COMPREPLY=($(compgen -W 'run build test ns config' -- \"$cur\"))"))
   }
 
   test("viash export cli_autocomplete Bash to file") {
-    val stdout = TestHelper.testMain(
+    TestHelper.testMain(
       "export", "cli_autocomplete",
       "--format", "bash",
       "--output", tempFile.toString
@@ -125,17 +125,17 @@ class MainExportSuite extends AnyFunSuite with BeforeAndAfter {
   }
 
   test("viash export cli_autocomplete Zsh") {
-    val stdout = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "export", "cli_autocomplete",
       "--format", "zsh"
     )
 
-    assert(stdout.startsWith("""#compdef viash"""))
-    assert(stdout.contains("_viash_export_commands"))
+    assert(testOutput.stdout.startsWith("""#compdef viash"""))
+    assert(testOutput.stdout.contains("_viash_export_commands"))
   }
 
   test("viash export cli_autocomplete Zsh to file") {
-    val stdout = TestHelper.testMain(
+    TestHelper.testMain(
       "export", "cli_autocomplete",
       "--format", "zsh",
       "--output", tempFile.toString
@@ -147,16 +147,16 @@ class MainExportSuite extends AnyFunSuite with BeforeAndAfter {
   }
 
   test("viash export config_schema") {
-    val stdout = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "export", "config_schema"
     )
 
-    assert(stdout.startsWith("""- - name: "__this__""""))
-    assert(stdout.contains("""type: "OneOrMore[String]""""))
+    assert(testOutput.stdout.startsWith("""- - name: "__this__""""))
+    assert(testOutput.stdout.contains("""type: "OneOrMore[String]""""))
   }
 
   test("viash export config_schema to file") {
-    val stdout = TestHelper.testMain(
+    TestHelper.testMain(
       "export", "config_schema",
       "--output", tempFile.toString
     )
@@ -167,25 +167,25 @@ class MainExportSuite extends AnyFunSuite with BeforeAndAfter {
   }
 
   test("viash export json_schema") {
-    val stdout = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "export", "json_schema"
     )
 
-    assert(stdout.startsWith("""$schema: "https://json-schema.org/draft-07/schema#""""))
-    assert(stdout.contains("""- $ref: "#/definitions/Config""""))
+    assert(testOutput.stdout.startsWith("""$schema: "https://json-schema.org/draft-07/schema#""""))
+    assert(testOutput.stdout.contains("""- $ref: "#/definitions/Config""""))
   }
 
   test("viash export json_schema, explicit yaml format") {
-    val stdout = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "export", "json_schema", "--format", "yaml"
     )
 
-    assert(stdout.startsWith("""$schema: "https://json-schema.org/draft-07/schema#""""))
-    assert(stdout.contains("""- $ref: "#/definitions/Config""""))
+    assert(testOutput.stdout.startsWith("""$schema: "https://json-schema.org/draft-07/schema#""""))
+    assert(testOutput.stdout.contains("""- $ref: "#/definitions/Config""""))
   }
 
   test("viash export json_schema to file, explicit yaml format") {
-    val stdout = TestHelper.testMain(
+    TestHelper.testMain(
       "export", "json_schema", "--format", "yaml",
       "--output", tempFile.toString
     )
@@ -196,20 +196,20 @@ class MainExportSuite extends AnyFunSuite with BeforeAndAfter {
   }
 
   test("viash export json_schema, json format") {
-    val stdout = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "export", "json_schema", "--format", "json"
     )
 
-    assert(stdout.startsWith(
+    assert(testOutput.stdout.startsWith(
         """{
           |  "$schema" : "https://json-schema.org/draft-07/schema#",
           |  "definitions" : {
           |""".stripMargin))
-    assert(stdout.contains(""""$ref" : "#/definitions/Config""""))
+    assert(testOutput.stdout.contains(""""$ref" : "#/definitions/Config""""))
   }
 
   test("viash export json_schema to file, json format") {
-    val stdout = TestHelper.testMain(
+    TestHelper.testMain(
       "export", "json_schema", "--format", "json",
       "--output", tempFile.toString
     )
diff --git a/src/test/scala/io/viash/e2e/help/MainHelpSuite.scala b/src/test/scala/io/viash/e2e/help/MainHelpSuite.scala
index a02c36f0a..d68012429 100644
--- a/src/test/scala/io/viash/e2e/help/MainHelpSuite.scala
+++ b/src/test/scala/io/viash/e2e/help/MainHelpSuite.scala
@@ -11,69 +11,69 @@ class MainHelpSuite extends AnyFunSuite{
   private val configFile = getClass.getResource(s"/testbash/config.vsh.yaml").getPath
 
   test("viash config view default functionality without help") {
-    val (stdout, _, _) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "config", "view",
       configFile
     )
 
-    assert(stdout.startsWith("functionality:"))
-    assert(stdout.contains("testbash"))
+    assert(testOutput.stdout.startsWith("functionality:"))
+    assert(testOutput.stdout.contains("testbash"))
   }
 
   test("viash config view default functionality leading help") {
-    val output = TestHelper.testMainException[ExitException](
+    val testOutput = TestHelper.testMainException[ExitException](
       "config", "view",
       "--help"
     )
 
-    assert(output.startsWith("viash config view"))
-    assert(!output.contains("testbash"))
+    assert(testOutput.stdout.startsWith("viash config view"))
+    assert(!testOutput.stdout.contains("testbash"))
   }
 
   test("viash config view default functionality trailing help") {
-    val output = TestHelper.testMainException[ExitException](
+    val testOutput = TestHelper.testMainException[ExitException](
       "config", "view",
       configFile,
       "--help"
     )
 
-    assert(output.startsWith("viash config view"))
-    assert(!output.contains("testbash"))
+    assert(testOutput.stdout.startsWith("viash config view"))
+    assert(!testOutput.stdout.contains("testbash"))
   }
 
   test("viash config view default functionality trailing help after platform argument") {
-    val output = TestHelper.testMainException[ExitException](
+    val testOutput = TestHelper.testMainException[ExitException](
       "config", "view",
       configFile,
-      "--platform", "native",
+      "--runner", "native",
       "--help"
     )
 
-    assert(output.startsWith("viash config view"))
-    assert(!output.contains("testbash"))
+    assert(testOutput.stdout.startsWith("viash config view"))
+    assert(!testOutput.stdout.contains("testbash"))
   }
 
   test("viash config view default functionality trailing help before platform argument") {
-    val output = TestHelper.testMainException[ExitException](
+    val testOutput = TestHelper.testMainException[ExitException](
       "config", "view",
       configFile,
       "--help",
-      "--platform", "native"
+      "--runner", "native"
     )
 
-    assert(output.startsWith("viash config view"))
-    assert(!output.contains("testbash"))
+    assert(testOutput.stdout.startsWith("viash config view"))
+    assert(!testOutput.stdout.contains("testbash"))
   }
 
 
   test("viash config view default functionality with --help as runner argument") {
-    val output = TestHelper.testMainException[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "config", "view",
       configFile,
       "--runner", "--help"
     )
 
-    assert(!output.contains("viash config view"))
+    assert(!testOutput.stdout.contains("viash config view"))
   }
 
 }
diff --git a/src/test/scala/io/viash/e2e/ns_build/MainNSBuildNativeSuite.scala b/src/test/scala/io/viash/e2e/ns_build/MainNSBuildNativeSuite.scala
index 17a50ba01..84911f228 100644
--- a/src/test/scala/io/viash/e2e/ns_build/MainNSBuildNativeSuite.scala
+++ b/src/test/scala/io/viash/e2e/ns_build/MainNSBuildNativeSuite.scala
@@ -34,7 +34,7 @@ class MainNSBuildNativeSuite extends AnyFunSuite with BeforeAndAfterAll{
 
   // convert testbash
   test("viash ns can build") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
     "ns", "build",
       "-s", nsPath,
       "-t", tempFolStr
@@ -42,7 +42,7 @@ class MainNSBuildNativeSuite extends AnyFunSuite with BeforeAndAfterAll{
 
     assert(nsFolder.exists)
     assert(nsFolder.isDirectory)
-    assert(exitCode == 1)
+    assert(testOutput.exitCode == Some(1))
 
     for ((component, _, _, _) <- components) {
       val executable = componentExecutableFile(component)
@@ -51,7 +51,7 @@ class MainNSBuildNativeSuite extends AnyFunSuite with BeforeAndAfterAll{
     }
 
     val regexBuildError = raw"Reading file \'.*/src/ns_error/config\.vsh\.yaml\' failed".r
-    assert(regexBuildError.findFirstIn(stderr).isDefined, "Expecting to get an error because of an invalid yaml in ns_error")
+    assert(regexBuildError.findFirstIn(testOutput.stderr).isDefined, "Expecting to get an error because of an invalid yaml in ns_error")
   }
 
   test("Check whether the executable can run") {
diff --git a/src/test/scala/io/viash/e2e/ns_exec/MainNSExecNativeSuite.scala b/src/test/scala/io/viash/e2e/ns_exec/MainNSExecNativeSuite.scala
index 946606b6c..21f0263ea 100644
--- a/src/test/scala/io/viash/e2e/ns_exec/MainNSExecNativeSuite.scala
+++ b/src/test/scala/io/viash/e2e/ns_exec/MainNSExecNativeSuite.scala
@@ -27,16 +27,15 @@ class MainNSExecNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
   private val tempFolStr = temporaryFolder.toString
 
   test("Check whether ns exec \\; works") {
-    val (stdoutRaw, stderrRaw, _) =
-      TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
         "ns", "exec",
         "--src", nsPath,
         "--apply_runner",
         "--apply_engine",
         "echo _{functionality-name}_ -{dir}- !{path}! ~{engine}~ ={namespace}=+\\;"
       )
-    val stdout = stdoutRaw.replaceAll(nsPath, "src/")
-    val stderr = stderrRaw.replaceAll(nsPath, "src/")
+    val stdout = testOutput.stdout.replaceAll(nsPath, "src/")
+    val stderr = testOutput.stderr.replaceAll(nsPath, "src/")
 
     for (component <- components) {
       val regexCommand = s"""\\+ echo _${component}_ -src/$component/?- !src/$component/config.vsh.yaml! ~native~ =testns=""".r
@@ -47,13 +46,13 @@ class MainNSExecNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
   }
 
   test("Check whether ns exec + works") {
-    val (stdoutRaw, stderrRaw, _) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "exec",
       "--src", nsPath,
       "echo {path} +"
     )
-    val stdout = stdoutRaw.replaceAll(nsPath, "src/")
-    val stderr = stderrRaw.replaceAll(nsPath, "src/")
+    val stdout = testOutput.stdout.replaceAll(nsPath, "src/")
+    val stderr = testOutput.stderr.replaceAll(nsPath, "src/")
 
     // can't guarantee order of components
     val regexCommand = s"""\\+ echo src/[^/]*/config.vsh.yaml src/[^/]*/config.vsh.yaml src/[^/]*/config.vsh.yaml src/[^/]*/config.vsh.yaml""".r
diff --git a/src/test/scala/io/viash/e2e/ns_list/MainNSListNativeSuite.scala b/src/test/scala/io/viash/e2e/ns_list/MainNSListNativeSuite.scala
index 5afbeeb7b..47a1b49cd 100644
--- a/src/test/scala/io/viash/e2e/ns_list/MainNSListNativeSuite.scala
+++ b/src/test/scala/io/viash/e2e/ns_list/MainNSListNativeSuite.scala
@@ -29,22 +29,22 @@ class MainNSListNativeSuite extends AnyFunSuite{
 
   // convert testbash
   test("viash ns list") {
-   val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+   val testOutput = TestHelper.testMain(
       "ns", "list",
       "-s", nsPath,
     )
 
-    assert(exitCode == 1)
+    assert(testOutput.exitCode == Some(1))
 
     for (component <- components) {
       val regexName = raw"""name:\s+"$component""""
-      assert(regexName.r.findFirstIn(stdout).isDefined, s"\nRegex: ${regexName}; text: \n$stdout")
+      assert(regexName.r.findFirstIn(testOutput.stdout).isDefined, s"\nRegex: ${regexName}; text: \n${testOutput.stdout}")
     }
 
     val regexBuildError = raw"Reading file \'.*/src/ns_error/config\.vsh\.yaml\' failed"
-    assert(regexBuildError.r.findFirstIn(stderr).isDefined, "Expecting to get an error because of an invalid yaml in ns_error")
+    assert(regexBuildError.r.findFirstIn(testOutput.stderr).isDefined, "Expecting to get an error because of an invalid yaml in ns_error")
 
-    val stdout2 = s"(?s)(\u001b.{4})?((Not all configs parsed successfully)|(All \\d+ configs parsed successfully)).*$$".r.replaceAllIn(stdout, "")
+    val stdout2 = s"(?s)(\u001b.{4})?((Not all configs parsed successfully)|(All \\d+ configs parsed successfully)).*$$".r.replaceAllIn(testOutput.stdout, "")
 
     val config = parser.parse(stdout2)
       .fold(throw _, _.as[Array[Config]])
@@ -59,7 +59,7 @@ class MainNSListNativeSuite extends AnyFunSuite{
     )
 
     for ((regex, count) <- samples) {
-      assert(regex.r.findAllMatchIn(stdout).size == count, s"Expecting $count hits on stdout of regex [$regex]")
+      assert(regex.r.findAllMatchIn(testOutput.stdout).size == count, s"Expecting $count hits on stdout of regex [$regex]")
     }
   }
 
@@ -67,44 +67,44 @@ class MainNSListNativeSuite extends AnyFunSuite{
 
   // convert testbash
   test("viash ns list filter by engine and runner") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "list",
       "-s", nsPath,
       "--engine", "docker",
       "--runner", "docker"
     )
 
-    assert(exitCode == 1)
-    val configs = parser.parse(stdout)
+    assert(testOutput.exitCode == Some(1))
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
     assert(configs.length == 0)
   }
   test("viash ns list filter by engine #2") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "list",
       "-s", scalaPath,
       "--engine", "docker",
       "--runner", "executable"
     )
 
-    assert(exitCode == 0)
+    assert(testOutput.exitCode == Some(0))
 
-    val configs = parser.parse(stdout)
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
     assert(configs.length == 1)
   }
   test("viash ns list filter by engine #3") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
      "ns", "list",
       "-s", scalaPath,
       "--engine", "not_exists",
       "--runner", "not_exists"
     )
 
-    assert(exitCode == 0)
-    val configs = parser.parse(stdout)
+    assert(testOutput.exitCode == Some(0))
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
     assert(configs.length == 0)
@@ -112,200 +112,200 @@ class MainNSListNativeSuite extends AnyFunSuite{
 
   // test query_name
   test("viash ns list query_name") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
      "ns", "list",
       "-s", nsPath,
       "--query_name", "ns_add"
     )
 
-    assert(exitCode == 1)
-    val configs = parser.parse(stdout)
+    assert(testOutput.exitCode == Some(1))
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
     assert(configs.length == 1)
-    assert(stdout.contains("name: \"ns_add\""))
+    assert(testOutput.stdout.contains("name: \"ns_add\""))
   }
 
   test("viash ns list query_name full match") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
      "ns", "list",
       "-s", nsPath,
       "--query_name", "^ns_add$"
     )
 
-    assert(exitCode == 1)
-    val configs = parser.parse(stdout)
+    assert(testOutput.exitCode == Some(1))
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
     assert(configs.length == 1)
-    assert(stdout.contains("name: \"ns_add\""))
+    assert(testOutput.stdout.contains("name: \"ns_add\""))
   }
 
   test("viash ns list query_name partial match") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "list",
       "-s", nsPath,
       "--query_name", "add"
     )
 
-    assert(exitCode == 1)
-    val configs = parser.parse(stdout)
+    assert(testOutput.exitCode == Some(1))
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
     assert(configs.length == 1)
-    assert(stdout.contains("name: \"ns_add\""))
+    assert(testOutput.stdout.contains("name: \"ns_add\""))
   }
 
   test("viash ns list query_name no match") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "list",
       "-s", nsPath,
       "--query_name", "foo"
     )
 
-    assert(exitCode == 1)
-    assert(stdout.trim() == "[]")
+    assert(testOutput.exitCode == Some(1))
+    assert(testOutput.stdout.trim() == "[]")
   }
 
   // test query
   test("viash ns list query") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "list",
       "-s", nsPath,
       "-q", "testns/ns_add"
     )
 
-    assert(exitCode == 1)
-    val configs = parser.parse(stdout)
+    assert(testOutput.exitCode == Some(1))
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
     assert(configs.length == 1)
-    assert(stdout.contains("name: \"ns_add\""))
+    assert(testOutput.stdout.contains("name: \"ns_add\""))
   }
 
   test("viash ns list query full match") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "list",
       "-s", nsPath,
       "-q", "^testns/ns_add$"
     )
 
-    assert(exitCode == 1)
-    val configs = parser.parse(stdout)
+    assert(testOutput.exitCode == Some(1))
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
     assert(configs.length == 1)
-    assert(stdout.contains("name: \"ns_add\""))
+    assert(testOutput.stdout.contains("name: \"ns_add\""))
   }
 
   test("viash ns list query partial match") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "list",
       "-s", nsPath,
       "-q", "test.*/.*add"
     )
 
-    assert(exitCode == 1)
-    val configs = parser.parse(stdout)
+    assert(testOutput.exitCode == Some(1))
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
     assert(configs.length == 1)
-    assert(stdout.contains("name: \"ns_add\""))
+    assert(testOutput.stdout.contains("name: \"ns_add\""))
   }
 
   test("viash ns list query only partial name") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "list",
       "-s", nsPath,
       "-q", "add"
     )
 
-    assert(exitCode == 1)
-    val configs = parser.parse(stdout)
+    assert(testOutput.exitCode == Some(1))
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
     assert(configs.length == 1)
-    assert(stdout.contains("name: \"ns_add\""))
+    assert(testOutput.stdout.contains("name: \"ns_add\""))
   }
 
   test("viash ns list query no match") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "list",
       "-s", nsPath,
       "-q", "foo"
     )
 
-    assert(exitCode == 1)
-    assert(stdout.trim() == "[]")
+    assert(testOutput.exitCode == Some(1))
+    assert(testOutput.stdout.trim() == "[]")
   }
 
   // test query_namespace
   test("viash ns list query_namespace") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
      "ns", "list",
       "-s", nsPath,
       "--query_namespace", "testns"
     )
 
-    assert(exitCode == 1)
-    val configs = parser.parse(stdout)
+    assert(testOutput.exitCode == Some(1))
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
 
     assert(configs.length == components.length)
-    assert(stdout.contains("name: \"ns_add\""))
-    assert(stdout.contains("name: \"ns_subtract\""))
-    assert(!stdout.contains("name: \"ns_error\""))
-    assert(!stdout.contains("name: \"ns_disabled\""))
+    assert(testOutput.stdout.contains("name: \"ns_add\""))
+    assert(testOutput.stdout.contains("name: \"ns_subtract\""))
+    assert(!testOutput.stdout.contains("name: \"ns_error\""))
+    assert(!testOutput.stdout.contains("name: \"ns_disabled\""))
   }
 
   test("viash ns list query_namespace full match") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
      "ns", "list",
       "-s", nsPath,
       "--query_namespace", "^testns$"
     )
 
-    assert(exitCode == 1)
-    val configs = parser.parse(stdout)
+    assert(testOutput.exitCode == Some(1))
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
 
     assert(configs.length == components.length)
-    assert(stdout.contains("name: \"ns_add\""))
-    assert(stdout.contains("name: \"ns_subtract\""))
-    assert(!stdout.contains("name: \"ns_error\""))
-    assert(!stdout.contains("name: \"ns_disabled\""))
+    assert(testOutput.stdout.contains("name: \"ns_add\""))
+    assert(testOutput.stdout.contains("name: \"ns_subtract\""))
+    assert(!testOutput.stdout.contains("name: \"ns_error\""))
+    assert(!testOutput.stdout.contains("name: \"ns_disabled\""))
   }
 
   test("viash ns list query_namespace partial match") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "list",
       "-s", nsPath,
       "--query_namespace", "test"
     )
 
-    assert(exitCode == 1)
-    val configs = parser.parse(stdout)
+    assert(testOutput.exitCode == Some(1))
+    val configs = parser.parse(testOutput.stdout)
       .fold(throw _, _.as[Array[Config]])
       .fold(throw _, identity)
 
     assert(configs.length == components.length)
-    assert(stdout.contains("name: \"ns_add\""))
-    assert(stdout.contains("name: \"ns_subtract\""))
-    assert(!stdout.contains("name: \"ns_error\""))
-    assert(!stdout.contains("name: \"ns_disabled\""))
+    assert(testOutput.stdout.contains("name: \"ns_add\""))
+    assert(testOutput.stdout.contains("name: \"ns_subtract\""))
+    assert(!testOutput.stdout.contains("name: \"ns_error\""))
+    assert(!testOutput.stdout.contains("name: \"ns_disabled\""))
   }
 
   test("viash ns list query_namespace no match") {
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "list",
       "-s", nsPath,
       "--query_namespace", "foo"
     )
 
-    assert(exitCode == 1)
-    assert(stdout.trim() == "[]")
+    assert(testOutput.exitCode == Some(1))
+    assert(testOutput.stdout.trim() == "[]")
   }
 
 }
diff --git a/src/test/scala/io/viash/e2e/ns_test/MainNSTestNativeSuite.scala b/src/test/scala/io/viash/e2e/ns_test/MainNSTestNativeSuite.scala
index dee8976ea..add2216bc 100644
--- a/src/test/scala/io/viash/e2e/ns_test/MainNSTestNativeSuite.scala
+++ b/src/test/scala/io/viash/e2e/ns_test/MainNSTestNativeSuite.scala
@@ -47,7 +47,7 @@ class MainNSTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
 
 
   test("Check namespace test output without working dir message") {
-    val (stdout, stderr, _) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "test",
       "--src", nsPath,
       "--keep", "false"
@@ -55,24 +55,24 @@ class MainNSTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
 
     // Test inclusion of a header
     val regexHeader = raw"^\s*namespace\s*functionality\s*runner\s*engine\s*test_name\s*exit_code\s*duration\s*result".r
-    assert(regexHeader.findFirstIn(stdout).isDefined, s"\nRegex: ${regexHeader.toString}; text: \n$stdout")
+    assert(regexHeader.findFirstIn(testOutput.stdout).isDefined, s"\nRegex: ${regexHeader.toString}; text: \n${testOutput.stdout}")
 
     for (
       (component, steps) <- components;
       (step, resultPattern) <- steps
     ) {
       val regex = s"""testns\\s*$component\\s*executable\\s*native\\s*$step$resultPattern""".r
-      assert(regex.findFirstIn(stdout).isDefined, s"\nRegex: '${regex.toString}'; text: \n$stdout")
+      assert(regex.findFirstIn(testOutput.stdout).isDefined, s"\nRegex: '${regex.toString}'; text: \n${testOutput.stdout}")
     }
 
     val regexBuildError = raw"Reading file \'.*/src/ns_error/config\.vsh\.yaml\' failed".r
-    assert(regexBuildError.findFirstIn(stderr).isDefined, "Expecting to get an error because of an invalid yaml in ns_error")
+    assert(regexBuildError.findFirstIn(testOutput.stderr).isDefined, "Expecting to get an error because of an invalid yaml in ns_error")
 
-    assert(stderr.contains("The status of the component 'ns_power' is set to deprecated."))
+    assert(testOutput.stderr.contains("The status of the component 'ns_power' is set to deprecated."))
   }
 
   test("Check namespace test output with working dir message") {
-    val (stdout, stderr, _) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "test",
       "--src", nsPath,
       "--keep", "true"
@@ -80,27 +80,27 @@ class MainNSTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
 
     // Test inclusion of a header
     val regexHeader = raw"^\s*namespace\s*functionality\s*runner\s*engine\s*test_name\s*exit_code\s*duration\s*result".r
-    assert(regexHeader.findFirstIn(stdout).isDefined, s"\nRegex: ${regexHeader.toString}; text: \n$stdout")
+    assert(regexHeader.findFirstIn(testOutput.stdout).isDefined, s"\nRegex: ${regexHeader.toString}; text: \n${testOutput.stdout}")
 
     val regexWdir = raw"The working directory for the namespace tests is [\w/]+[\r\n]{1,2}".r
-    assert(regexWdir.findFirstIn(stderr).isDefined, s"\nRegex: ${regexHeader.toString}; text: \n$stderr")
+    assert(regexWdir.findFirstIn(testOutput.stderr).isDefined, s"\nRegex: ${regexHeader.toString}; text: \n${testOutput.stderr}")
 
     for (
       (component, steps) <- components;
       (step, resultPattern) <- steps
     ) {
       val regex = s"""testns\\s*$component\\s*executable\\s*native\\s*$step$resultPattern""".r
-      assert(regex.findFirstIn(stdout).isDefined, s"\nRegex: '${regex.toString}'; text: \n$stdout")
+      assert(regex.findFirstIn(testOutput.stdout).isDefined, s"\nRegex: '${regex.toString}'; text: \n${testOutput.stdout}")
     }
 
     val regexBuildError = raw"Reading file \'.*/src/ns_error/config\.vsh\.yaml\' failed".r
-    assert(regexBuildError.findFirstIn(stderr).isDefined, "Expecting to get an error because of an invalid yaml in ns_error")
+    assert(regexBuildError.findFirstIn(testOutput.stderr).isDefined, "Expecting to get an error because of an invalid yaml in ns_error")
   }
 
   test("Check namespace test output with tsv option") {
     val log = Paths.get(tempFolStr, "log.tsv").toFile
 
-    val (testText, _, _) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "ns", "test",
       "--tsv", log.toString,
       "--src", nsPath
@@ -133,7 +133,7 @@ class MainNSTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
     val fileHeader = "Test header" + sys.props("line.separator")
     Files.write(log.toPath, fileHeader.getBytes(StandardCharsets.UTF_8))
 
-    val (testText, _, _) = TestHelper.testMainWithStdErr(
+    TestHelper.testMain(
       "ns", "test",
       "--tsv", log.toString,
       "--append",
@@ -166,7 +166,7 @@ class MainNSTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
   test("Check namespace test output with tsv and append options without the output file exists") {
     val log = Paths.get(tempFolStr, "log_append_new.tsv").toFile
 
-    val (testText, _, _) = TestHelper.testMainWithStdErr(
+    TestHelper.testMain(
       "ns", "test",
       "--tsv", log.toString,
       "--append",
diff --git a/src/test/scala/io/viash/e2e/run/RunComputationalRequirements.scala b/src/test/scala/io/viash/e2e/run/RunComputationalRequirements.scala
index 768ca2dbf..6e01480f8 100644
--- a/src/test/scala/io/viash/e2e/run/RunComputationalRequirements.scala
+++ b/src/test/scala/io/viash/e2e/run/RunComputationalRequirements.scala
@@ -15,105 +15,105 @@ class RunComputationalRequirements extends AnyFunSuite with BeforeAndAfterAll {
   private val configDeriver = ConfigDeriver(Paths.get(configFile), temporaryFolder)
   
   test("Check without computational requirements") {
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "run",
       configFile
     )
 
-    assert(output.contains("cpus unset"))
-    assert(output.contains("memory unset"))
+    assert(testOutput.stdout.contains("cpus unset"))
+    assert(testOutput.stdout.contains("memory unset"))
   }
 
   test("Check set cpus in CLI") {
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "run",
       "--cpus", "2",
       configFile
     )
 
-    assert(output.contains("cpus: 2"))
-    assert(output.contains("memory unset"))
+    assert(testOutput.stdout.contains("cpus: 2"))
+    assert(testOutput.stdout.contains("memory unset"))
   }
 
   test("Check set memory in CLI") {
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "run",
       "--memory", "2mb",
       configFile
     )
 
-    assert(output.contains("cpus unset"))
-    assert(output.contains("memory: 2"))
+    assert(testOutput.stdout.contains("cpus unset"))
+    assert(testOutput.stdout.contains("memory: 2"))
   }
 
   test("Check set cpus in config") {
     val newConfigFilePath = configDeriver.derive(""".functionality.requirements := {cpus: 3}""", "cpus_set")
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "run",
       newConfigFilePath
     )
 
-    assert(output.contains("cpus: 3"))
-    assert(output.contains("memory unset"))
+    assert(testOutput.stdout.contains("cpus: 3"))
+    assert(testOutput.stdout.contains("memory unset"))
   }
 
   test("Check set memory in config") {
     val newConfigFilePath = configDeriver.derive(""".functionality.requirements := {memory: "3 mb"}""", "memory_set")
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "run",
       newConfigFilePath
     )
 
-    assert(output.contains("cpus unset"))
-    assert(output.contains("memory: 3"))
+    assert(testOutput.stdout.contains("cpus unset"))
+    assert(testOutput.stdout.contains("memory: 3"))
   }
 
   test("Check set cpus and memory in config") {
     val newConfigFilePath = configDeriver.derive(""".functionality.requirements := {cpus: 3, memory: "3 mb"}""", "cpus_memory_set")
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "run",
       newConfigFilePath
     )
 
-    assert(output.contains("cpus: 3"))
-    assert(output.contains("memory: 3"))
+    assert(testOutput.stdout.contains("cpus: 3"))
+    assert(testOutput.stdout.contains("memory: 3"))
   }
 
   test("Check set cpus in config and CLI") {
     val newConfigFilePath = configDeriver.derive(""".functionality.requirements := {cpus: 3}""", "cpus_set2")
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "run",
       "--cpus", "2",
       newConfigFilePath
     )
 
-    assert(output.contains("cpus: 2"))
-    assert(output.contains("memory unset"))
+    assert(testOutput.stdout.contains("cpus: 2"))
+    assert(testOutput.stdout.contains("memory unset"))
   }
 
   test("Check set memory in config and CLI") {
     val newConfigFilePath = configDeriver.derive(""".functionality.requirements := {memory: "3 mb"}""", "memory_set2")
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "run",
       "--memory", "2mb",
       newConfigFilePath
     )
 
-    assert(output.contains("cpus unset"))
-    assert(output.contains("memory: 2"))
+    assert(testOutput.stdout.contains("cpus unset"))
+    assert(testOutput.stdout.contains("memory: 2"))
   }
 
   test("Check set cpus and memory in config and CLI") {
     val newConfigFilePath = configDeriver.derive(""".functionality.requirements := {cpus: 3, memory: "3 mb"}""", "cpus_memory_set2")
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "run",
       "--cpus", "2",
       "--memory", "2mb",
       newConfigFilePath
     )
 
-    assert(output.contains("cpus: 2"))
-    assert(output.contains("memory: 2"))
+    assert(testOutput.stdout.contains("cpus: 2"))
+    assert(testOutput.stdout.contains("memory: 2"))
   }
 
   override def afterAll(): Unit = {
diff --git a/src/test/scala/io/viash/e2e/test/MainTestDockerSuite.scala b/src/test/scala/io/viash/e2e/test/MainTestDockerSuite.scala
index 92c85ec00..e575be536 100644
--- a/src/test/scala/io/viash/e2e/test/MainTestDockerSuite.scala
+++ b/src/test/scala/io/viash/e2e/test/MainTestDockerSuite.scala
@@ -22,37 +22,37 @@ class MainTestDockerSuite extends AnyFunSuite with BeforeAndAfterAll with Parall
   private val configDeriver = ConfigDeriver(Paths.get(configFile), temporaryFolder)
 
   test("Check standard test output for typical outputs", DockerTest) {
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "docker",
       "--runner", "docker",
       configFile
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Check standard test output with trailing arguments", DockerTest) {
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       configFile,
       "--engine", "docker",
       "--runner", "docker"
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Check standard test output with leading and trailing arguments", DockerTest) {
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "docker",
       "--runner", "docker",
@@ -60,17 +60,17 @@ class MainTestDockerSuite extends AnyFunSuite with BeforeAndAfterAll with Parall
       "-k", "false"
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Check setup strategy", DockerTest) {
     val newConfigFilePath = configDeriver.derive(""".engines[.type == "docker" && !has(.id) ].setup := [{ type: "docker", run: "echo 'Hello world!'" }]""", "cache_config")
     // first run to create cache entries
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "docker",
       "--runner", "docker",
@@ -79,7 +79,7 @@ class MainTestDockerSuite extends AnyFunSuite with BeforeAndAfterAll with Parall
     )
 
     // Do a second run to check if forcing a docker build using setup works
-    val testTextNoCaching = TestHelper.testMain(
+    val testOutputNoCaching = TestHelper.testMain(
       "test",
       "--engine", "docker",
       "--runner", "docker",
@@ -89,10 +89,10 @@ class MainTestDockerSuite extends AnyFunSuite with BeforeAndAfterAll with Parall
     )
 
     val regexBuildCache = raw"\n#\d \[\d/\d\] RUN echo 'Hello world!'\n#\d CACHED\n".r
-    assert(!regexBuildCache.findFirstIn(testTextNoCaching).isDefined, "Expected to not find caching.")
+    assert(!regexBuildCache.findFirstIn(testOutputNoCaching.stdout).isDefined, "Expected to not find caching.")
 
     // Do a third run to check caching
-    val testTextCaching = TestHelper.testMain(
+    val testOutputCaching = TestHelper.testMain(
       "test",
       "--engine", "docker",
       "--runner", "docker",
@@ -103,10 +103,10 @@ class MainTestDockerSuite extends AnyFunSuite with BeforeAndAfterAll with Parall
 
     // retry once if it failed
     val testTextCachingWithRetry = 
-      if (regexBuildCache.findFirstIn(testTextCaching).isDefined) {
-        testTextCaching
+      if (regexBuildCache.findFirstIn(testOutputCaching.stdout).isDefined) {
+        testOutputCaching
       } else {
-        checkTempDirAndRemove(testTextCaching, false)
+        checkTempDirAndRemove(testOutputCaching.stdout, false)
         
         TestHelper.testMain(
           "test",
@@ -118,62 +118,62 @@ class MainTestDockerSuite extends AnyFunSuite with BeforeAndAfterAll with Parall
         )
       }
 
-    assert(regexBuildCache.findFirstIn(testTextCachingWithRetry).isDefined, "Expected to find caching.")
+    assert(regexBuildCache.findFirstIn(testTextCachingWithRetry.stdout).isDefined, "Expected to find caching.")
 
-    checkTempDirAndRemove(testText, false)
-    checkTempDirAndRemove(testTextNoCaching, false)
-    checkTempDirAndRemove(testTextCachingWithRetry, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
+    checkTempDirAndRemove(testOutputNoCaching.stdout, false)
+    checkTempDirAndRemove(testTextCachingWithRetry.stdout, false)
   }
 
   test("Verify base config derivation", NativeTest) {
     val newConfigFilePath = configDeriver.derive(Nil, "default_config")
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Check failing build", DockerTest) {
     val newConfigFilePath = configDeriver.derive(""".engines[.type == "docker" && !has(.id) ].setup := [{ type: "apt", packages: ["get_the_machine_that_goes_ping"] }]""", "failed_build")
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "test",
       "--engine", "docker",
       "--runner", "docker",
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText == "Setup failed!")
+    assert(testOutput.exceptionText.get == "Setup failed!")
 
-    assert(testOutput.output.contains("Running tests in temporary directory: "))
-    assert(testOutput.output.contains("ERROR! Setup failed!"))
-    assert(!testOutput.output.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("ERROR! Setup failed!"))
+    assert(!testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testOutput.output, true)
+    checkTempDirAndRemove(testOutput.stdout, true)
   }
 
   test("Check config and resource files with spaces in the filename", DockerTest) {
     val newConfigFilePath = Paths.get(tempFolStr, "config with spaces.vsh.yaml")
     Files.copy(Paths.get(configFile), newConfigFilePath)
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "docker",
       "--runner", "docker",
       newConfigFilePath.toString()
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   /**
diff --git a/src/test/scala/io/viash/e2e/test/MainTestNativeSuite.scala b/src/test/scala/io/viash/e2e/test/MainTestNativeSuite.scala
index 075d8a507..423456ad3 100644
--- a/src/test/scala/io/viash/e2e/test/MainTestNativeSuite.scala
+++ b/src/test/scala/io/viash/e2e/test/MainTestNativeSuite.scala
@@ -10,6 +10,8 @@ import org.scalatest.funsuite.AnyFunSuite
 
 import scala.reflect.io.Directory
 import sys.process._
+import io.viash.exceptions.ConfigParserException
+import io.viash.exceptions.MissingResourceFileException
 
 class MainTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
   Logger.UseColorOverride.value = Some(false)
@@ -23,37 +25,37 @@ class MainTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
   private val configInvalidYamlFile = getClass.getResource("/testbash/invalid_configs/config_invalid_yaml.vsh.yaml").getPath
 
   test("Check standard test output for typical outputs") {
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "native",
       "--runner", "native",
       configFile
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Check standard test output with trailing arguments") {
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       configFile,
       "--engine", "native",
       "--runner", "native"
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Check standard test output with leading and trailing arguments") {
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "native",
       "--runner", "native",
@@ -61,243 +63,243 @@ class MainTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
       "-k", "false"
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Verify base config derivation") {
     val newConfigFilePath = configDeriver.derive(Nil, "default_config")
 
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Check test output when no tests are specified in the functionality file") {
     val newConfigFilePath = configDeriver.derive("del(.functionality.test_resources)", "no_tests")
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("WARNING! No tests found!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("WARNING! No tests found!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Check test output when a test fails") {
     val newConfigFilePath = configDeriver.derive(""".functionality.test_resources[.path == "tests/check_outputs.sh"].path := "tests/fail_failed_test.sh"""", "failed_test")
-    val testText = TestHelper.testMainException[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("ERROR! Only 1 out of 2 test scripts succeeded!"))
-    assert(!testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("ERROR! Only 1 out of 2 test scripts succeeded!"))
+    assert(!testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, true)
+    checkTempDirAndRemove(testOutput.stdout, true)
   }
 
   test("Check test output when test doesn't exist") {
     val newConfigFilePath = configDeriver.derive(""".functionality.test_resources[.path == "tests/check_outputs.sh"].path := "tests/nonexistent_test.sh"""", "nonexisting_test")
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText == "Only 1 out of 2 test scripts succeeded!")
+    assert(testOutput.exceptionText.get == "Only 1 out of 2 test scripts succeeded!")
 
-    assert(testOutput.output.contains("Running tests in temporary directory: "))
-    assert(testOutput.output.contains("ERROR! Only 1 out of 2 test scripts succeeded!"))
-    assert(!testOutput.output.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("ERROR! Only 1 out of 2 test scripts succeeded!"))
+    assert(!testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testOutput.output, true)
+    checkTempDirAndRemove(testOutput.stdout, true)
   }
 
   test("Check config and resource files with spaces in the filename") {
     val newConfigFilePath = Paths.get(tempFolStr, "config with spaces.vsh.yaml")
     Files.copy(Paths.get(configFile), newConfigFilePath)
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath.toString()
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Check config file without 'functionality' specified") {
     val newConfigFilePath = configDeriver.derive("""del(.functionality)""", "missing_functionality")
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText.contains("must be a yaml file containing a viash config."))
-    assert(testOutput.output.isEmpty)
+    assert(testOutput.exceptionText.get.contains("must be a yaml file containing a viash config."))
+    assert(testOutput.stdout.isEmpty)
   }
 
   test("Check invalid runner type") {
     val newConfigFilePath = configDeriver.derive(""".runners += { type: "foo" }""", "invalid_runner_type")
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[ConfigParserException](
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText.contains("Type 'foo' is not recognised. Valid types are 'executable', and 'nextflow'."))
-    assert(testOutput.exceptionText.contains(
+    assert(testOutput.exceptionText.get.contains("Type 'foo' is not recognised. Valid types are 'executable', and 'nextflow'."))
+    assert(testOutput.exceptionText.get.contains(
       """{
         |  "type" : "foo"
         |}""".stripMargin))
-    assert(testOutput.output.isEmpty)
+    assert(testOutput.stdout.isEmpty)
   }
 
   test("Check invalid engine type") {
     val newConfigFilePath = configDeriver.derive(""".engines += { type: "foo" }""", "invalid_engine_type")
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[ConfigParserException](
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText.contains("Type 'foo' is not recognised. Valid types are 'docker', and 'native'."))
-    assert(testOutput.exceptionText.contains(
+    assert(testOutput.exceptionText.get.contains("Type 'foo' is not recognised. Valid types are 'docker', and 'native'."))
+    assert(testOutput.exceptionText.get.contains(
       """{
         |  "type" : "foo"
         |}""".stripMargin))
-    assert(testOutput.output.isEmpty)
+    assert(testOutput.stdout.isEmpty)
   }
 
   test("Check invalid platform type") {
     val newConfigFilePath = configDeriver.derive(""".platforms := [{ type: "foo" }]""", "invalid_platform_type")
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[ConfigParserException](
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText.contains("Type 'foo' is not recognised. Valid types are 'docker', 'native', and 'nextflow'."))
-    assert(testOutput.exceptionText.contains(
+    assert(testOutput.exceptionText.get.contains("Type 'foo' is not recognised. Valid types are 'docker', 'native', and 'nextflow'."))
+    assert(testOutput.exceptionText.get.contains(
       """{
         |  "type" : "foo"
         |}""".stripMargin))
-    assert(testOutput.output.isEmpty)
+    assert(testOutput.stdout.isEmpty)
   }
 
   test("Check invalid field in runner") {
     val newConfigFilePath = configDeriver.derive(""".runners += { type: "executable", foo: "bar" }""", "invalid_runner_field")
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[ConfigParserException](
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText.contains("Invalid data fields for ExecutableRunner."))
-    assert(testOutput.exceptionText.contains(
+    assert(testOutput.exceptionText.get.contains("Invalid data fields for ExecutableRunner."))
+    assert(testOutput.exceptionText.get.contains(
       """{
         |  "type" : "executable",
         |  "foo" : "bar"
         |}""".stripMargin))
-    assert(testOutput.output.isEmpty)
+    assert(testOutput.stdout.isEmpty)
   }
 
   test("Check invalid field in engine") {
     val newConfigFilePath = configDeriver.derive(""".engines += { type: "native", foo: "bar" }""", "invalid_engine_field")
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[ConfigParserException](
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText.contains("Invalid data fields for NativeEngine."))
-    assert(testOutput.exceptionText.contains(
+    assert(testOutput.exceptionText.get.contains("Invalid data fields for NativeEngine."))
+    assert(testOutput.exceptionText.get.contains(
       """{
         |  "type" : "native",
         |  "foo" : "bar"
         |}""".stripMargin))
-    assert(testOutput.output.isEmpty)
+    assert(testOutput.stdout.isEmpty)
   }
 
   test("Check invalid field in platform") {
     val newConfigFilePath = configDeriver.derive(""".platforms := [{ type: "native", foo: "bar" }]""", "invalid_platform_field")
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[ConfigParserException](
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText.contains("Invalid data fields for NativePlatform."))
-    assert(testOutput.exceptionText.contains(
+    assert(testOutput.exceptionText.get.contains("Invalid data fields for NativePlatform."))
+    assert(testOutput.exceptionText.get.contains(
       """{
         |  "type" : "native",
         |  "foo" : "bar"
         |}""".stripMargin))
-    assert(testOutput.output.isEmpty)
+    assert(testOutput.stdout.isEmpty)
   }
 
   test("Check valid viash config yaml but with wrong file extension") {
     val newConfigFilePath = Paths.get(tempFolStr, "config.txt")
     Files.copy(Paths.get(configFile), newConfigFilePath)
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath.toString()
     )
 
-    assert(testOutput.exceptionText.contains("must be a yaml file containing a viash config."))
-    assert(testOutput.output.isEmpty)
+    assert(testOutput.exceptionText.get.contains("must be a yaml file containing a viash config."))
+    assert(testOutput.stdout.isEmpty)
   }
 
   test("Check invalid viash config yaml") {
-    val testOutput = TestHelper.testMainException2[io.circe.ParsingFailure](
+    val testOutput = TestHelper.testMainException[org.yaml.snakeyaml.parser.ParserException](
       "test",
       "--engine", "native",
       "--runner", "native",
       configInvalidYamlFile
     )
 
-    assert(testOutput.exceptionText.contains("while parsing a flow mapping"))
-    assert(testOutput.output.isEmpty)
+    assert(testOutput.exceptionText.get.contains("while parsing a flow mapping"))
+    assert(testOutput.stdout.isEmpty)
   }
 
   test("Check output in case --keep true is specified") {
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "native",
       "--runner", "native",
@@ -305,15 +307,15 @@ class MainTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
       configFile
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(!testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(!testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, true)
+    checkTempDirAndRemove(testOutput.stdout, true)
   }
 
   test("Check output in case --keep false is specified") {
-    val testText = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "native",
       "--runner", "native",
@@ -321,16 +323,16 @@ class MainTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
       configFile
     )
 
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Check test output when a test fails and --keep true is specified") {
     val newConfigFilePath = configDeriver.derive(""".functionality.test_resources[.path == "tests/check_outputs.sh"].path := "tests/fail_failed_test.sh"""", "failed_test_keep_true")
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "test",
       "--engine", "native",
       "--runner", "native",
@@ -338,13 +340,13 @@ class MainTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText == "Only 1 out of 2 test scripts succeeded!")
+    assert(testOutput.exceptionText.get == "Only 1 out of 2 test scripts succeeded!")
 
-    assert(testOutput.output.contains("Running tests in temporary directory: "))
-    assert(testOutput.output.contains("ERROR! Only 1 out of 2 test scripts succeeded!"))
-    assert(!testOutput.output.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("ERROR! Only 1 out of 2 test scripts succeeded!"))
+    assert(!testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testOutput.output, true)
+    checkTempDirAndRemove(testOutput.stdout, true)
   }
 
   test("Check test output when a test fails and --keep false is specified") {
@@ -352,7 +354,7 @@ class MainTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
       """.functionality.test_resources[.path == "tests/check_outputs.sh"].path := "tests/fail_failed_test.sh"""",
       "failed_test_keep_false"
     )
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "test",
       "--engine", "native",
       "--runner", "native",
@@ -360,69 +362,69 @@ class MainTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText == "Only 1 out of 2 test scripts succeeded!")
+    assert(testOutput.exceptionText.get == "Only 1 out of 2 test scripts succeeded!")
 
-    assert(testOutput.output.contains("Running tests in temporary directory: "))
-    assert(testOutput.output.contains("ERROR! Only 1 out of 2 test scripts succeeded!"))
-    assert(testOutput.output.contains("Cleaning up temporary directory"))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("ERROR! Only 1 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    checkTempDirAndRemove(testOutput.output, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Check deprecation warning") {
     val newConfigFilePath = configDeriver.derive(""".functionality.status := "deprecated"""", "deprecated")
-    val (testText, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(exitCode == 0)
-    assert(testText.contains("Running tests in temporary directory: "))
-    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
-    assert(testText.contains("Cleaning up temporary directory"))
+    assert(testOutput.exitCode == Some(0))
+    assert(testOutput.stdout.contains("Running tests in temporary directory: "))
+    assert(testOutput.stdout.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testOutput.stdout.contains("Cleaning up temporary directory"))
 
-    assert(stderr.contains("The status of the component 'testbash' is set to deprecated."))
+    assert(testOutput.stderr.contains("The status of the component 'testbash' is set to deprecated."))
     
-    checkTempDirAndRemove(testText, false)
+    checkTempDirAndRemove(testOutput.stdout, false)
   }
 
   test("Check standard test output with bad engine name") {
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "test",
       "--engine", "non_existing_engine",
       "--runner", "native",
       configFile
     )
 
-    assert(testOutput.exceptionText == "no engine id matching regex 'non_existing_engine' could not be found in the config.")
-    assert(testOutput.output.isEmpty)
+    assert(testOutput.exceptionText.get == "no engine id matching regex 'non_existing_engine' could not be found in the config.")
+    assert(testOutput.stdout.isEmpty)
   }
 
   test("Check standard test output with bad runner name") {
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[RuntimeException](
       "test",
       "--engine", "native",
       "--runner", "non_existing_runner",
       configFile
     )
 
-    assert(testOutput.exceptionText == "no runner id matching regex 'non_existing_runner' could not be found in the config.")
-    assert(testOutput.output.isEmpty)
+    assert(testOutput.exceptionText.get == "no runner id matching regex 'non_existing_runner' could not be found in the config.")
+    assert(testOutput.stdout.isEmpty)
   }
 
   test("Check standard test output with missing test resource") {
     val newConfigFilePath = configDeriver.derive(""".functionality.test_resources += { type: 'file', path: 'foobar.txt' }""", "deprecated")
 
-    val testOutput = TestHelper.testMainException2[RuntimeException](
+    val testOutput = TestHelper.testMainException[MissingResourceFileException](
       "test",
       "--engine", "native",
       "--runner", "native",
       newConfigFilePath
     )
 
-    assert(testOutput.exceptionText.matches("Missing resource .*foobar\\.txt as specified in .*"))
+    assert(testOutput.exceptionText.get.matches("Missing resource .*foobar\\.txt as specified in .*"))
   }
 
   /**
diff --git a/src/test/scala/io/viash/e2e/test/TestComputationalRequirements.scala b/src/test/scala/io/viash/e2e/test/TestComputationalRequirements.scala
index b8a7f48cc..85c25d6fb 100644
--- a/src/test/scala/io/viash/e2e/test/TestComputationalRequirements.scala
+++ b/src/test/scala/io/viash/e2e/test/TestComputationalRequirements.scala
@@ -15,105 +15,105 @@ class TestComputationalRequirements extends AnyFunSuite with BeforeAndAfterAll {
   private val configDeriver = ConfigDeriver(Paths.get(configFile), temporaryFolder)
   
   test("Check without computational requirements") {
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       configFile
     )
 
-    assert(output.contains("cpus unset"))
-    assert(output.contains("memory unset"))
+    assert(testOutput.stdout.contains("cpus unset"))
+    assert(testOutput.stdout.contains("memory unset"))
   }
 
   test("Check set cpus in CLI") {
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--cpus", "2",
       configFile
     )
 
-    assert(output.contains("cpus: 2"))
-    assert(output.contains("memory unset"))
+    assert(testOutput.stdout.contains("cpus: 2"))
+    assert(testOutput.stdout.contains("memory unset"))
   }
 
   test("Check set memory in CLI") {
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--memory", "2mb",
       configFile
     )
 
-    assert(output.contains("cpus unset"))
-    assert(output.contains("memory: 2"))
+    assert(testOutput.stdout.contains("cpus unset"))
+    assert(testOutput.stdout.contains("memory: 2"))
   }
 
   test("Check set cpus in config") {
     val newConfigFilePath = configDeriver.derive(""".functionality.requirements := {cpus: 3}""", "cpus_set")
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       newConfigFilePath
     )
 
-    assert(output.contains("cpus: 3"))
-    assert(output.contains("memory unset"))
+    assert(testOutput.stdout.contains("cpus: 3"))
+    assert(testOutput.stdout.contains("memory unset"))
   }
 
   test("Check set memory in config") {
     val newConfigFilePath = configDeriver.derive(""".functionality.requirements := {memory: "3 mb"}""", "memory_set")
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       newConfigFilePath
     )
 
-    assert(output.contains("cpus unset"))
-    assert(output.contains("memory: 3"))
+    assert(testOutput.stdout.contains("cpus unset"))
+    assert(testOutput.stdout.contains("memory: 3"))
   }
 
   test("Check set cpus and memory in config") {
     val newConfigFilePath = configDeriver.derive(""".functionality.requirements := {cpus: 3, memory: "3 mb"}""", "cpus_memory_set")
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       newConfigFilePath
     )
 
-    assert(output.contains("cpus: 3"))
-    assert(output.contains("memory: 3"))
+    assert(testOutput.stdout.contains("cpus: 3"))
+    assert(testOutput.stdout.contains("memory: 3"))
   }
 
   test("Check set cpus in config and CLI") {
     val newConfigFilePath = configDeriver.derive(""".functionality.requirements := {cpus: 3}""", "cpus_set2")
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--cpus", "2",
       newConfigFilePath
     )
 
-    assert(output.contains("cpus: 2"))
-    assert(output.contains("memory unset"))
+    assert(testOutput.stdout.contains("cpus: 2"))
+    assert(testOutput.stdout.contains("memory unset"))
   }
 
   test("Check set memory in config and CLI") {
     val newConfigFilePath = configDeriver.derive(""".functionality.requirements := {memory: "3 mb"}""", "memory_set2")
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--memory", "2mb",
       newConfigFilePath
     )
 
-    assert(output.contains("cpus unset"))
-    assert(output.contains("memory: 2"))
+    assert(testOutput.stdout.contains("cpus unset"))
+    assert(testOutput.stdout.contains("memory: 2"))
   }
 
   test("Check set cpus and memory in config and CLI") {
     val newConfigFilePath = configDeriver.derive(""".functionality.requirements := {cpus: 3, memory: "3 mb"}""", "cpus_memory_set2")
-    val output = TestHelper.testMain(
+    val testOutput = TestHelper.testMain(
       "test",
       "--cpus", "2",
       "--memory", "2mb",
       newConfigFilePath
     )
 
-    assert(output.contains("cpus: 2"))
-    assert(output.contains("memory: 2"))
+    assert(testOutput.stdout.contains("cpus: 2"))
+    assert(testOutput.stdout.contains("memory: 2"))
   }
 
   override def afterAll(): Unit = {
diff --git a/src/test/scala/io/viash/functionality/dependencies/Dependency.scala b/src/test/scala/io/viash/functionality/dependencies/Dependency.scala
index bb1c9fe1c..12199bceb 100644
--- a/src/test/scala/io/viash/functionality/dependencies/Dependency.scala
+++ b/src/test/scala/io/viash/functionality/dependencies/Dependency.scala
@@ -56,13 +56,123 @@ class DependencyTest extends AnyFunSuite with BeforeAndAfterAll {
     writeTestConfig(testFolder.resolve("src/dep2/config.vsh.yaml"), fun2)
 
     // build
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
         "ns", "build",
         "-s", testFolder.resolve("src").toString(),
         "-t", testFolder.resolve("target").toString()
       )
 
-    assert(stderr.strip == "All 2 configs built successfully", "check build was successful")
+    assert(testOutput.stderr.strip == "All 2 configs built successfully", "check build was successful")
+
+    // check file & file content
+    val outputPath = testFolder.resolve("target/executable/dep2/dep2")
+    val executable = outputPath.toFile
+    assert(executable.exists)
+    assert(executable.canExecute)
+
+    val outputText = IO.read(outputPath.toUri())
+    assert(outputText.contains("VIASH_DEP_DEP1="), "check the dependency is set in the output script")
+
+    // check output when running
+    val out = Exec.runCatch(
+      Seq(executable.toString)
+    )
+
+    assert(out.output == "Hello from dep1\nHello from dep2\n")
+    assert(out.exitValue == 0)
+  }
+
+  test("Use a local repository with an absolute path") {
+    val testFolder = createViashSubFolder(temporaryFolder, "local_test_absolute_path")
+    
+    // write test files
+    val fun1 = Functionality(
+      name = "dep1",
+      resources = textBashScript("echo Hello from dep1"),
+    )
+    val fun2 = Functionality(
+      name = "dep2",
+      resources = textBashScript("$dep_dep1\necho Hello from dep2"),
+      dependencies = List(Dependency("dep1", repository = Right(LocalRepository(path = Some("/dependencies")))))
+    )
+
+    writeTestConfig(testFolder.resolve("dependencies/src/dep1/config.vsh.yaml"), fun1)
+    writeTestConfig(testFolder.resolve("src/dep2/config.vsh.yaml"), fun2)
+
+    // build our local repository
+    val build1 = TestHelper.testMain(
+        workingDir = Some(testFolder.resolve("dependencies")),
+        "ns", "build",
+        "-s", testFolder.resolve("dependencies/src").toString(),
+        "-t", testFolder.resolve("dependencies/target").toString()
+      )
+    
+    assert(build1.stderr.strip == "All 1 configs built successfully", "check dependency build was successful")
+
+    // build
+    val build2 = TestHelper.testMain(
+        workingDir = Some(testFolder),
+        "ns", "build",
+        "-s", testFolder.resolve("src").toString(),
+        "-t", testFolder.resolve("target").toString()
+      )
+
+    assert(build2.stderr.strip == "All 1 configs built successfully", "check build was successful")
+
+    // check file & file content
+    val outputPath = testFolder.resolve("target/executable/dep2/dep2")
+    val executable = outputPath.toFile
+    assert(executable.exists)
+    assert(executable.canExecute)
+
+    val outputText = IO.read(outputPath.toUri())
+    assert(outputText.contains("VIASH_DEP_DEP1="), "check the dependency is set in the output script")
+
+    // check output when running
+    val out = Exec.runCatch(
+      Seq(executable.toString)
+    )
+
+    assert(out.output == "Hello from dep1\nHello from dep2\n")
+    assert(out.exitValue == 0)
+  }
+
+  test("Use a local repository with a relative path") {
+    val testFolder = createViashSubFolder(temporaryFolder, "local_test_absolute_path")
+    
+    // write test files
+    val fun1 = Functionality(
+      name = "dep1",
+      resources = textBashScript("echo Hello from dep1"),
+    )
+    val fun2 = Functionality(
+      name = "dep2",
+      resources = textBashScript("$dep_dep1\necho Hello from dep2"),
+      dependencies = List(Dependency("dep1", repository = Right(LocalRepository(path = Some("../../dependencies")))))
+    )
+
+    writeTestConfig(testFolder.resolve("dependencies/src/dep1/config.vsh.yaml"), fun1)
+    writeTestConfig(testFolder.resolve("src/dep2/config.vsh.yaml"), fun2)
+
+    // build our local repository
+    val build1 = TestHelper.testMain(
+        workingDir = Some(testFolder.resolve("dependencies")),
+        "ns", "build",
+        "-s", testFolder.resolve("dependencies/src").toString(),
+        "-t", testFolder.resolve("dependencies/target").toString()
+      )
+    
+    assert(build1.stderr.strip == "All 1 configs built successfully", "check dependency build was successful")
+
+    // build
+    val build2 = TestHelper.testMain(
+        workingDir = Some(testFolder),
+        "ns", "build",
+        "-s", testFolder.resolve("src").toString(),
+        "-t", testFolder.resolve("target").toString()
+      )
+
+    assert(build2.stderr.strip == "All 1 configs built successfully", "check build was successful")
 
     // check file & file content
     val outputPath = testFolder.resolve("target/executable/dep2/dep2")
@@ -95,13 +205,13 @@ class DependencyTest extends AnyFunSuite with BeforeAndAfterAll {
     writeTestConfig(testFolder.resolve("src/dep3/config.vsh.yaml"), fun)
 
     // build
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
         "ns", "build",
         "-s", testFolder.resolve("src").toString(),
         "-t", testFolder.resolve("target").toString()
       )
 
-    assert(stderr.strip.contains("All 1 configs built successfully"), "check build was successful")
+    assert(testOutput.stderr.strip.contains("All 1 configs built successfully"), "check build was successful")
 
     // check file & file content
     val outputPath = testFolder.resolve("target/executable/dep3/dep3")
@@ -134,13 +244,13 @@ class DependencyTest extends AnyFunSuite with BeforeAndAfterAll {
     writeTestConfig(testFolder.resolve("src/dep4/config.vsh.yaml"), fun)
 
     // build
-    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
         "ns", "build",
         "-s", testFolder.resolve("src").toString(),
         "-t", testFolder.resolve("target").toString()
       )
 
-    assert(stderr.strip.contains("All 1 configs built successfully"), "check build was successful")
+    assert(testOutput.stderr.strip.contains("All 1 configs built successfully"), "check build was successful")
 
     // check file & file content
     val outputPath = testFolder.resolve("target/executable/dep4/dep4")
diff --git a/src/test/scala/io/viash/runners/nextflow/NextflowScriptTest.scala b/src/test/scala/io/viash/runners/nextflow/NextflowScriptTest.scala
index 55f213787..8bb48fcbf 100644
--- a/src/test/scala/io/viash/runners/nextflow/NextflowScriptTest.scala
+++ b/src/test/scala/io/viash/runners/nextflow/NextflowScriptTest.scala
@@ -36,9 +36,7 @@ class NextflowScriptTest extends AnyFunSuite with BeforeAndAfterAll {
 
   test("Build pipeline components", DockerTest, NextflowTest) {
     // build the nextflow containers
-    // TODO: use the correct CWD to build the pipeline to be ablke
-    // to detect the correct path to the _viash.yaml file
-    val (_, _, _) = TestHelper.testMainWithStdErr(
+    TestHelper.testMain(
       "ns", "build",
       "-s", srcPath,
       "-t", targetPath,
diff --git a/src/test/scala/io/viash/runners/nextflow/Vdsl3ModuleTest.scala b/src/test/scala/io/viash/runners/nextflow/Vdsl3ModuleTest.scala
index 92144e98d..c048348c7 100644
--- a/src/test/scala/io/viash/runners/nextflow/Vdsl3ModuleTest.scala
+++ b/src/test/scala/io/viash/runners/nextflow/Vdsl3ModuleTest.scala
@@ -35,7 +35,7 @@ class Vdsl3ModuleTest extends AnyFunSuite with BeforeAndAfterAll {
 
   test("Build pipeline components", DockerTest, NextflowTest) {
     // build the nextflow containers
-    val (_, _, _) = TestHelper.testMainWithStdErr(
+    TestHelper.testMain(
       "ns", "build",
       "--runner", "nextflow",
       "-s", srcPath,
@@ -101,15 +101,15 @@ class Vdsl3ModuleTest extends AnyFunSuite with BeforeAndAfterAll {
     val correctedStdOut2 = regex.matcher(correctedStdOut1).replaceAll("")
 
     // run Viash's --help
-    val (stdOut2, stdErr2, exitCode2) = TestHelper.testMainWithStdErr(
+    val testOutput = TestHelper.testMain(
       "run", workflowsPath + "/pipeline3/config.vsh.yaml",
       "--", "--help"
     )
 
-    assert(exitCode2 == 0)
+    assert(testOutput.exitCode == Some(0))
 
     // check if they are the same
-    assert(correctedStdOut2 == stdOut2)
+    assert(correctedStdOut2 == testOutput.stdout)
   }
 
   override def afterAll(): Unit = {
diff --git a/src/test/scala/io/viash/runners/nextflow/Vdsl3StandaloneTest.scala b/src/test/scala/io/viash/runners/nextflow/Vdsl3StandaloneTest.scala
index 93447eeb8..31260ac98 100644
--- a/src/test/scala/io/viash/runners/nextflow/Vdsl3StandaloneTest.scala
+++ b/src/test/scala/io/viash/runners/nextflow/Vdsl3StandaloneTest.scala
@@ -35,7 +35,7 @@ class Vdsl3StandaloneTest extends AnyFunSuite with BeforeAndAfterAll {
 
   test("Build pipeline components", DockerTest, NextflowTest) {
     // build the nextflow containers
-    val (_, _, _) = TestHelper.testMainWithStdErr(
+    TestHelper.testMain(
       "ns", "build",
       "-s", srcPath,
       "-t", targetPath,
diff --git a/src/test/scala/io/viash/runners/nextflow/WorkflowHelperTest.scala b/src/test/scala/io/viash/runners/nextflow/WorkflowHelperTest.scala
index 8a12836b9..ad9a3e9c1 100644
--- a/src/test/scala/io/viash/runners/nextflow/WorkflowHelperTest.scala
+++ b/src/test/scala/io/viash/runners/nextflow/WorkflowHelperTest.scala
@@ -37,7 +37,7 @@ class WorkflowHelperTest extends AnyFunSuite with BeforeAndAfterAll {
 
   test("Build pipeline components", DockerTest, NextflowTest) {
     // build the nextflow containers
-    val (_, _, _) = TestHelper.testMainWithStdErr(
+    TestHelper.testMain(
       "ns", "build",
       "-s", srcPath,
       "-t", targetPath,