diff --git a/.github/workflows/sbt_test.yml b/.github/workflows/sbt_test.yml
index 54a9a3547..6182f0ead 100644
--- a/.github/workflows/sbt_test.yml
+++ b/.github/workflows/sbt_test.yml
@@ -42,12 +42,19 @@ jobs:
           processx
           testthat
 
-    - name: Set up sbt
+    - name: Set up java & sbt
       uses: actions/setup-java@v4
       with:
         distribution: temurin
         java-version: ${{ matrix.java.ver }}
 
+    - name: Set up sbt specifically on macOS on arm64 if needed
+      if: ${{ runner.os == 'macOS' && runner.arch == 'ARM64'}}
+      run: |
+        if ! command -v sbt &> /dev/null; then
+          brew install sbt
+        fi
+
     - name: Set up Scala
       run: |
         if [[ "${{ matrix.config.os }}" =~ ^macos.*$ ]]; then
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6b8e10f29..ea727c960 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,10 +1,44 @@
+# Viash 0.8.6 (2024-04-26): Bug fixes and improvements for CI
+
+Fix some issues in some edge cases.
+Add options for testing in a CI environment. Given that these options are not meant for general use, they are hidden from the help message.
+Some improvements are made to run in Nextflow Fusion.
+
+## DOCUMENTATION
+
+* `docker setup strategy`: Fix inconsistencies in the documentation (PR #657).
+
+* `repositories`: Fix `uri` -> `repo` in the repositories documentation (PR #682).
+
+## NEW FUNCTIONALITY
+
+* `viash test` and `viash ns test`: Add a hidden `--dry_run` option to build the tests without executing them (PR #676).
+
+* `viash test` and `viash ns test`: Add a hidden `--deterministic_working directory` argument to use a fixed directory path (PR #683).
+
+* `component names`: Verify that component namespace and name combinations are unique (PR #685).
+
+## BUG FIXES
+
+* `NextflowPlatform`: Fix publishing state for output arguments with `multiple: true` (#638, PR #639). 
+
+* `Executable`: Check whether a multiple output file argument contains a wildcard (PR #639).
+
+* `NextflowPlatform`: Fix a possible cause of concurrency issues (PR #669).
+
+* `Resources`: Fix an issue where if the first resource is not a script, the resource is silently dropped (PR #670).
+
+* `Docker automount`: Prevent adding a trailing slash to an automounted folder (PR #673).
+
+* `NextflowPlatform`: Change the at-runtime generated nextflow process from an in-memory to an on-disk temporary file, which should cause less issues with Nextflow Fusion (PR #681).
+
 # Viash 0.8.5 (2024-02-21): Bug fixes and documentation improvements
 
 Fix a bug when building a test docker container which requires a test resource. Additional improvements for the website documentation and support for the latest version of Nextflow are added.
 
 ## BUG FIXES
 
-* `nextflow runner`: Fix an issue with current nextflow-latest (24.01.0-edge) where our supporting library passes a GString instead of a String and results in a type mismatch (PR #640).
+* `NextflowPlatform`: Fix an issue with current nextflow-latest (24.01.0-edge) where our supporting library passes a GString instead of a String and results in a type mismatch (PR #640).
 
 * `test resources`: Make non-script test resources available during building of a docker container for `viash test` (PR #652).
 
diff --git a/build.sbt b/build.sbt
index fb5ab9abc..14a4e3b8e 100644
--- a/build.sbt
+++ b/build.sbt
@@ -1,6 +1,6 @@
 name := "viash"
 
-version := "0.8.5"
+version := "0.8.6"
 
 scalaVersion := "2.13.10"
 
diff --git a/src/main/resources/io/viash/helpers/bashutils/ViashAutodetectMount.sh b/src/main/resources/io/viash/helpers/bashutils/ViashAutodetectMount.sh
index d47d74983..e46a4ed51 100644
--- a/src/main/resources/io/viash/helpers/bashutils/ViashAutodetectMount.sh
+++ b/src/main/resources/io/viash/helpers/bashutils/ViashAutodetectMount.sh
@@ -15,7 +15,11 @@ function ViashAutodetectMount {
     base_name=`basename "$abs_path"`
   fi
   mount_target="/viash_automount$mount_source"
-  echo "$mount_target/$base_name"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
 }
 function ViashAutodetectMountArg {
   abs_path=$(ViashAbsolutePath "$1")
diff --git a/src/main/resources/io/viash/platforms/nextflow/DataflowHelper.nf b/src/main/resources/io/viash/platforms/nextflow/DataflowHelper.nf
index 464a3062d..450ad7492 100644
--- a/src/main/resources/io/viash/platforms/nextflow/DataflowHelper.nf
+++ b/src/main/resources/io/viash/platforms/nextflow/DataflowHelper.nf
@@ -52,16 +52,16 @@ def setWorkflowArguments(Map args) {
         // determine splitargs
         def splitArgs = args.
           collectEntries{procKey, dataKeys -> 
-          // dataKeys is a map but could also be a list
-          newSplitData = dataKeys
-            .collectEntries{ val ->
-              newKey = val instanceof String ? val : val.key
-              origKey = val instanceof String ? val : val.value
-              [ newKey, data[origKey] ]
-            }
-            .findAll{it.value}
-          [procKey, newSplitData]
-        }
+            // dataKeys is a map but could also be a list
+            def newSplitData = dataKeys
+              .collectEntries{ val ->
+                newKey = val instanceof String ? val : val.key
+                origKey = val instanceof String ? val : val.value
+                [ newKey, data[origKey] ]
+              }
+              .findAll{it.value}
+            [procKey, newSplitData]
+          }
 
         // return output
         [ id, newData, splitArgs] + passthrough
diff --git a/src/main/resources/io/viash/platforms/nextflow/VDSL3Helper.nf b/src/main/resources/io/viash/platforms/nextflow/VDSL3Helper.nf
index b774bfffb..306a74e93 100644
--- a/src/main/resources/io/viash/platforms/nextflow/VDSL3Helper.nf
+++ b/src/main/resources/io/viash/platforms/nextflow/VDSL3Helper.nf
@@ -84,7 +84,7 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
           .findAll { it.type == "file" && it.direction == "output" }
           .indexed()
           .collectEntries{ index, par ->
-            out = output[index + 1]
+            def out = output[index + 1]
             // strip dummy '.exitcode' file from output (see nextflow-io/nextflow#2678)
             if (!out instanceof List || out.size() <= 1) {
               if (par.multiple) {
@@ -210,7 +210,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   def inputFileExports = meta.config.functionality.allArguments
     .findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
     .collect { par ->
-      viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
+      def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
       "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
     }
 
@@ -266,7 +266,6 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   |  .join("\\n")
   |\"\"\"
   |# meta exports
-  |# export VIASH_META_RESOURCES_DIR="\${resourcesDir.toRealPath().toAbsolutePath()}"
   |export VIASH_META_RESOURCES_DIR="\${resourcesDir}"
   |export VIASH_META_TEMP_DIR="${['docker', 'podman', 'charliecloud'].any{ it == workflow.containerEngine } ? '/tmp' : tmpDir}"
   |export VIASH_META_FUNCTIONALITY_NAME="${meta.config.functionality.name}"
@@ -308,19 +307,22 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   //   println("######################\n$procStr\n######################")
   // }
 
-  // create runtime process
-  def ownerParams = new nextflow.script.ScriptBinding.ParamsMap()
-  def binding = new nextflow.script.ScriptBinding().setParams(ownerParams)
-  def module = new nextflow.script.IncludeDef.Module(name: procKey)
+  // write process to temp file
+  def tempFile = java.nio.file.Files.createTempFile("viash-process-${procKey}-", ".nf")
+  addShutdownHook { java.nio.file.Files.deleteIfExists(tempFile) }
+  tempFile.text = procStr
+
+  // create process from temp file
+  def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def scriptParser = new nextflow.script.ScriptParser(session)
+  def parser = new nextflow.script.ScriptParser(session)
     .setModule(true)
     .setBinding(binding)
-  scriptParser.scriptPath = scriptMeta.getScriptPath()
-  def moduleScript = scriptParser.runScript(procStr)
+  def moduleScript = parser.runScript(tempFile)
     .getScript()
 
   // register module in meta
+  def module = new nextflow.script.IncludeDef.Module(name: procKey)
   scriptMeta.addModule(moduleScript, module.name, module.alias)
 
   // retrieve and return process from meta
diff --git a/src/main/resources/io/viash/platforms/nextflow/arguments/_checkArgumentType.nf b/src/main/resources/io/viash/platforms/nextflow/arguments/_checkArgumentType.nf
index ca8125d75..569363331 100644
--- a/src/main/resources/io/viash/platforms/nextflow/arguments/_checkArgumentType.nf
+++ b/src/main/resources/io/viash/platforms/nextflow/arguments/_checkArgumentType.nf
@@ -114,7 +114,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     }
     expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
-    // cast to boolean if need ben
+    // cast to boolean if need be
     if (value instanceof String) {
       def valueLower = value.toLowerCase()
       if (valueLower == "true") {
diff --git a/src/main/resources/io/viash/platforms/nextflow/channel/_splitParams.nf b/src/main/resources/io/viash/platforms/nextflow/channel/_splitParams.nf
index 440380474..6bf055e87 100644
--- a/src/main/resources/io/viash/platforms/nextflow/channel/_splitParams.nf
+++ b/src/main/resources/io/viash/platforms/nextflow/channel/_splitParams.nf
@@ -18,13 +18,13 @@ Map<String, Object> _splitParams(Map<String, Object> parValues, Map config){
     }
     if (parameterSettings.multiple) { // Check if parameter can accept multiple values
       if (parValue instanceof Collection) {
-          parValue = parValue.collect{it instanceof String ? it.split(parameterSettings.multiple_sep) : it }
+        parValue = parValue.collect{it instanceof String ? it.split(parameterSettings.multiple_sep) : it }
       } else if (parValue instanceof String) {
-          parValue = parValue.split(parameterSettings.multiple_sep)
+        parValue = parValue.split(parameterSettings.multiple_sep)
       } else if (parValue == null) {
-          parValue = []
+        parValue = []
       } else {
-          parValue = [ parValue ]
+        parValue = [ parValue ]
       }
       parValue = parValue.flatten()
     }
diff --git a/src/main/resources/io/viash/platforms/nextflow/channel/channelFromParams.nf b/src/main/resources/io/viash/platforms/nextflow/channel/channelFromParams.nf
index 0d7881668..21d486382 100644
--- a/src/main/resources/io/viash/platforms/nextflow/channel/channelFromParams.nf
+++ b/src/main/resources/io/viash/platforms/nextflow/channel/channelFromParams.nf
@@ -60,9 +60,9 @@ private List<Tuple2<String, Map<String, Object>>> _paramsToParamSets(Map params,
     // Process ID
     def id = tup[0] ?: globalID
   
-    if (workflow.stubRun) {
+    if (workflow.stubRun && !id) {
       // if stub run, explicitly add an id if missing
-      id = id ? id : "stub${index}"
+      id = "stub${index}"
     }
     assert id != null: "Each parameter set should have at least an 'id'"
 
diff --git a/src/main/resources/io/viash/platforms/nextflow/channel/runComponents.nf b/src/main/resources/io/viash/platforms/nextflow/channel/runComponents.nf
index 0effeb6fb..e8467187c 100644
--- a/src/main/resources/io/viash/platforms/nextflow/channel/runComponents.nf
+++ b/src/main/resources/io/viash/platforms/nextflow/channel/runComponents.nf
@@ -77,6 +77,7 @@ def runComponents(Map args) {
         ? out_ch | map{tup ->
           def output = tup[1]
           def old_state = tup[2]
+          def new_state = null
           if (toState_ instanceof Map) {
             new_state = old_state + toState_.collectEntries{ key0, key1 ->
               [key0, output[key1]]
diff --git a/src/main/resources/io/viash/platforms/nextflow/functions/_stringIsAbsolutePath.nf b/src/main/resources/io/viash/platforms/nextflow/functions/_stringIsAbsolutePath.nf
index d3a339561..a6a1223f0 100644
--- a/src/main/resources/io/viash/platforms/nextflow/functions/_stringIsAbsolutePath.nf
+++ b/src/main/resources/io/viash/platforms/nextflow/functions/_stringIsAbsolutePath.nf
@@ -9,7 +9,7 @@
   * @return Whether the path is absolute, as a boolean.
   */
 def _stringIsAbsolutePath(path) {
-  _resolve_URL_PROTOCOL = ~/^([a-zA-Z][a-zA-Z0-9]*:)?\\/.+/
+  def _resolve_URL_PROTOCOL = ~/^([a-zA-Z][a-zA-Z0-9]*:)?\\/.+/
 
   assert path instanceof String
   return _resolve_URL_PROTOCOL.matcher(path).matches()
diff --git a/src/main/resources/io/viash/platforms/nextflow/readwrite/readCsv.nf b/src/main/resources/io/viash/platforms/nextflow/readwrite/readCsv.nf
index 9726f35e7..0b33f7013 100644
--- a/src/main/resources/io/viash/platforms/nextflow/readwrite/readCsv.nf
+++ b/src/main/resources/io/viash/platforms/nextflow/readwrite/readCsv.nf
@@ -38,7 +38,7 @@ def readCsv(file_path) {
         if (field == "") {
           return null
         }
-        m = removeQuote.matcher(field)
+        def m = removeQuote.matcher(field)
         if (m.find()) {
           return m.replaceFirst('$1')
         } else {
diff --git a/src/main/resources/io/viash/platforms/nextflow/states/findStates.nf b/src/main/resources/io/viash/platforms/nextflow/states/findStates.nf
index 1e1b2b17c..226691bca 100644
--- a/src/main/resources/io/viash/platforms/nextflow/states/findStates.nf
+++ b/src/main/resources/io/viash/platforms/nextflow/states/findStates.nf
@@ -1,5 +1,4 @@
 def findStates(Map params, Map config) {
-  // TODO: do a deep clone of config
   def auto_config = deepClone(config)
   def auto_params = deepClone(params)
 
diff --git a/src/main/resources/io/viash/platforms/nextflow/states/publishStates.nf b/src/main/resources/io/viash/platforms/nextflow/states/publishStates.nf
index 4e556b84d..cbc36b509 100644
--- a/src/main/resources/io/viash/platforms/nextflow/states/publishStates.nf
+++ b/src/main/resources/io/viash/platforms/nextflow/states/publishStates.nf
@@ -53,20 +53,20 @@ def publishStates(Map args) {
           def state_ = tup[1]
 
           // the input files and the target output filenames
-          def inputOutputFiles_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputOutputFiles_[0]
-          def outputFiles_ = inputOutputFiles_[1]
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
             .replaceAll('\\$key', key_)
 
-            // TODO: do the pathnames in state_ match up with the outputFiles_?
+            // TODO: do the pathnames in state_ match up with the outputFilenames_?
 
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFiles_]
+          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
         }
         | publishStatesProc
     emit: input_ch
@@ -99,12 +99,12 @@ process publishStatesProc {
       }
     }
   """
-  mkdir -p "\$(dirname '${yamlFile}')"
-  echo "Storing state as yaml"
-  echo '${yamlBlob}' > '${yamlFile}'
-  echo "Copying output files to destination folder"
-  ${copyCommands.join("\n  ")}
-  """
+mkdir -p "\$(dirname '${yamlFile}')"
+echo "Storing state as yaml"
+echo '${yamlBlob}' > '${yamlFile}'
+echo "Copying output files to destination folder"
+${copyCommands.join("\n  ")}
+"""
 }
 
 
@@ -133,9 +133,13 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$key', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, srcPath, destPath] tuples, where
-          //   - key, value is part of the state to be saved to disk
-          //   - srcPath and destPath are lists of files to be copied from src to dest
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (key, value) are the tuples that will be saved to the state.yaml file
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.functionality.allArguments
               .findAll { it.direction == "output" }
@@ -152,7 +156,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, srcPath: [], destPath: []]]
+                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -175,15 +179,16 @@ def publishStatesByConfig(Map args) {
                   // the index of the file
                   assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
                   def outputPerFile = value.withIndex().collect{ val, ix ->
-                    def value_ = java.nio.file.Paths.get(filename.replace("*", ix.toString()))
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def value_ = java.nio.file.Paths.get(filename_ix)
                     // if id contains a slash
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def srcPath = val instanceof File ? val.toPath() : val
-                    [value: value_, srcPath: srcPath, destPath: destPath]
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
                   }
-                  def transposedOutputs = ["value", "srcPath", "destPath"].collectEntries{ key -> 
+                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
                     [key, outputPerFile.collect{dic -> dic[key]}]
                   }
                   return [[key: plainName_] + transposedOutputs]
@@ -193,22 +198,22 @@ def publishStatesByConfig(Map args) {
                   if (yamlDir != null) {
                     value_ = yamlDir.relativize(value_)
                   }
-                  def srcPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, srcPath: [srcPath], destPath: [filename]]]
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
                 }
               }
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputFiles_ = processedState.collectMany{it.srcPath}
-          def outputFiles_ = processedState.collectMany{it.destPath}
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFiles_]
+          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
         }
         | publishStatesProc
     emit: input_ch
   }
   return publishStatesSimpleWf
-}
\ No newline at end of file
+}
diff --git a/src/main/resources/io/viash/platforms/nextflow/workflowFactory/workflowFactory.nf b/src/main/resources/io/viash/platforms/nextflow/workflowFactory/workflowFactory.nf
index 7061c42d8..26c50ad69 100644
--- a/src/main/resources/io/viash/platforms/nextflow/workflowFactory/workflowFactory.nf
+++ b/src/main/resources/io/viash/platforms/nextflow/workflowFactory/workflowFactory.nf
@@ -15,7 +15,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
     take: input_
 
     main:
-    chModified = input_
+    def chModified = input_
       | checkUniqueIds([:])
       | _debug(workflowArgs, "input")
       | map { tuple ->
@@ -102,12 +102,14 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         tuple
       }
 
-    chModifiedFiltered = workflowArgs.filter ?
+    def chModifiedFiltered = workflowArgs.filter ?
       chModified | filter{workflowArgs.filter(it)} :
       chModified
 
+    def chRun = null
+    def chPassthrough = null
     if (workflowArgs.runIf) {
-      runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModifiedFiltered.branch{ tup ->
         run: workflowArgs.runIf(tup[0], tup[1])
         passthrough: true
       }
@@ -118,7 +120,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       chPassthrough = Channel.empty()
     }
 
-    chArgs = workflowArgs.fromState ? 
+    def chArgs = workflowArgs.fromState ? 
       chRun | map{
         def new_data = workflowArgs.fromState(it.take(2))
         [it[0], new_data]
@@ -126,7 +128,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       chRun | map {tup -> tup.take(2)}
 
     // fill in defaults
-    chArgsWithDefaults = chArgs
+    def chArgsWithDefaults = chArgs
       | map { tuple ->
         def id_ = tuple[0]
         def data_ = tuple[1]
@@ -164,7 +166,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    chInitialOutput = chArgsWithDefaults
+    def chInitialOutput = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
@@ -194,7 +196,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       // | view{"chInitialOutput: ${it.take(3)}"}
 
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -203,7 +205,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      chPublish = chNewState
+      def chPublish = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
diff --git a/src/main/scala/io/viash/Main.scala b/src/main/scala/io/viash/Main.scala
index 858592407..01ccb2420 100644
--- a/src/main/scala/io/viash/Main.scala
+++ b/src/main/scala/io/viash/Main.scala
@@ -244,13 +244,18 @@ object Main extends Logging {
       case List(cli.test) =>
         val (config, platform) = readConfig(cli.test, project = proj1)
         val config2 = singleConfigDependencies(config, platform, None, proj1.rootDir)
+        if (cli.test.dryRun.getOrElse(false) && !cli.test.keep.toOption.map(_.toBoolean).getOrElse(false)) {
+          info("Warning: --dry_run is set, but --keep is not set. This will result in the generated files being deleted after the test.")
+        }
         ViashTest(
           config2,
           platform = platform.get,
           keepFiles = cli.test.keep.toOption.map(_.toBoolean),
           setupStrategy = cli.test.setup.toOption,
           cpus = cli.test.cpus.toOption,
-          memory = cli.test.memory.toOption
+          memory = cli.test.memory.toOption,
+          dryRun = cli.test.dryRun.toOption,
+          deterministicWorkingDirectory = cli.test.deterministicWorkingDirectory.toOption
         )
         0 // Exceptions are thrown when a test fails, so then the '0' is not returned but a '1'. Can be improved further.
       case List(cli.namespace, cli.namespace.build) =>
@@ -271,6 +276,9 @@ object Main extends Logging {
       case List(cli.namespace, cli.namespace.test) =>
         val (configs, allConfigs) = readConfigs(cli.namespace.test, project = proj1)
         val configs2 = namespaceDependencies(configs, allConfigs, None, proj1.rootDir)
+        if (cli.namespace.test.dryRun.getOrElse(false) && !cli.namespace.test.keep.toOption.map(_.toBoolean).getOrElse(false)) {
+          info("Warning: --dry_run is set, but --keep is not set. This will result in the generated files being deleted after the test.")
+        }
         val testResults = ViashNamespace.test(
           configs = configs2,
           parallel = cli.namespace.test.parallel(),
@@ -280,6 +288,8 @@ object Main extends Logging {
           cpus = cli.namespace.test.cpus.toOption,
           memory = cli.namespace.test.memory.toOption,
           setup = cli.namespace.test.setup.toOption,
+          dryRun = cli.namespace.test.dryRun.toOption,
+          deterministicWorkingDirectory = cli.namespace.test.deterministicWorkingDirectory.toOption,
         )
         val errors = testResults.flatMap(_.toOption).count(_.isError)
         if (errors > 0) 1 else 0
@@ -390,8 +400,7 @@ object Main extends Logging {
             Some(ViashNamespace.targetOutputPath(
               targetDir = td,
               platformId = pl,
-              namespace = config.functionality.namespace,
-              functionalityName = config.functionality.name
+              config = config
             ))
           case _ => None
         }
diff --git a/src/main/scala/io/viash/ViashNamespace.scala b/src/main/scala/io/viash/ViashNamespace.scala
index 451bf02e1..da930ccff 100644
--- a/src/main/scala/io/viash/ViashNamespace.scala
+++ b/src/main/scala/io/viash/ViashNamespace.scala
@@ -51,6 +51,9 @@ object ViashNamespace extends Logging {
         list.foreach(f)
   }
 
+  def targetOutputPath(targetDir: String, platformId: String, config: Config): String =
+    targetOutputPath(targetDir, platformId, config.functionality.namespace, config.functionality.name)
+
   def targetOutputPath(
     targetDir: String,
     platformId: String,
@@ -86,7 +89,7 @@ object ViashNamespace extends Logging {
             if (flatten) {
               target
             } else {
-              targetOutputPath(target, platformId, ns, funName)
+              targetOutputPath(target, platformId, conf)
             }
           val nsStr = ns.map(" (" + _ + ")").getOrElse("")
           infoOut(s"Exporting $funName$nsStr =$platformId=> $out")
@@ -113,7 +116,9 @@ object ViashNamespace extends Logging {
     tsv: Option[String] = None,
     append: Boolean = false,
     cpus: Option[Int],
-    memory: Option[String]
+    memory: Option[String],
+    dryRun: Option[Boolean] = None,
+    deterministicWorkingDirectory: Option[String] = None
   ): List[Either[(Config, ManyTestOutput), Status]] = {
     val configs1 = configs.filter{tup => tup match {
       // remove nextflow because unit testing nextflow modules
@@ -134,7 +139,11 @@ object ViashNamespace extends Logging {
     val tsvExists = tsvPath.exists(Files.exists(_))
     val tsvWriter = tsvPath.map(Files.newBufferedWriter(_, StandardOpenOption.CREATE, StandardOpenOption.WRITE, StandardOpenOption.APPEND))
 
-    val parentTempPath = IO.makeTemp("viash_ns_test")
+    val parentTempPath = IO.makeTemp(
+      name = deterministicWorkingDirectory.getOrElse("viash_ns_test"),
+      parentTempPath = None,
+      addRandomized = deterministicWorkingDirectory.isEmpty
+    )
     if (keepFiles.getOrElse(true)) {
       info(s"The working directory for the namespace tests is ${parentTempPath.toString()}")
     }
@@ -173,6 +182,7 @@ object ViashNamespace extends Logging {
             val namespace = conf.functionality.namespace.getOrElse("")
             val funName = conf.functionality.name
             val platName = platform.id
+            val directoryName = if(namespace.isEmpty) funName else namespace.replace('/', '_') + "_" + funName
 
             // print start message
             infoOut("%20s %20s %20s %20s %9s %8s %20s".format(namespace, funName, platName, "start", "", "", ""))
@@ -189,7 +199,9 @@ object ViashNamespace extends Logging {
                 quiet = true,
                 parentTempPath = Some(parentTempPath),
                 cpus = cpus,
-                memory = memory
+                memory = memory,
+                dryRun = dryRun,
+                deterministicWorkingDirectory = Some(directoryName)
               )
             } catch {
               case e: MissingResourceFileException => 
diff --git a/src/main/scala/io/viash/ViashTest.scala b/src/main/scala/io/viash/ViashTest.scala
index 56f7df88d..afbbc601a 100644
--- a/src/main/scala/io/viash/ViashTest.scala
+++ b/src/main/scala/io/viash/ViashTest.scala
@@ -67,10 +67,16 @@ object ViashTest extends Logging {
     verbosityLevel: Int = 6,
     parentTempPath: Option[Path] = None, 
     cpus: Option[Int], 
-    memory: Option[String]
+    memory: Option[String],
+    dryRun: Option[Boolean] = None,
+    deterministicWorkingDirectory: Option[String] = None,
   ): ManyTestOutput = {
     // create temporary directory
-    val dir = IO.makeTemp("viash_test_" + config.functionality.name, parentTempPath)
+    val dir = IO.makeTemp(
+      name = deterministicWorkingDirectory.getOrElse(s"viash_test_${config.functionality.name}_"),
+      parentTempPath = parentTempPath,
+      addRandomized = deterministicWorkingDirectory.isEmpty
+    )
     if (!quiet) infoOut(s"Running tests in temporary directory: '$dir'")
 
     // set version to temporary value
@@ -98,7 +104,8 @@ object ViashTest extends Logging {
       setupStrategy = setupStrategy.getOrElse("cachedbuild"),
       verbosityLevel = verbosityLevel,
       cpus = cpus,
-      memory = memory
+      memory = memory,
+      dryRun = dryRun
     )
     val count = results.count(_.exitValue == 0)
     val anyErrors = setupRes.exists(_.exitValue > 0) || count < results.length
@@ -147,7 +154,8 @@ object ViashTest extends Logging {
     setupStrategy: String, 
     verbosityLevel: Int, 
     cpus: Option[Int], 
-    memory: Option[String]
+    memory: Option[String],
+    dryRun: Option[Boolean]
   ): ManyTestOutput = {
     val fun = config.functionality
 
@@ -317,7 +325,10 @@ object ViashTest extends Logging {
           val subTmp = Paths.get(newDir.toString, "tmp")
           Files.createDirectories(subTmp)
 
-          val cmd = Seq(executable) ++ Seq(cpus.map("---cpus=" + _), memory.map("---memory="+_)).flatMap(a => a)
+          val cmd = if (dryRun.getOrElse(false))
+            Seq("echo", "Running dummy test script")
+          else
+            Seq(executable) ++ Seq(cpus.map("---cpus=" + _), memory.map("---memory="+_)).flatMap(a => a)
           logger(s"+${cmd.mkString(" ")}")
           val exitValue = Process(
             cmd,
@@ -340,4 +351,5 @@ object ViashTest extends Logging {
 
     ManyTestOutput(buildResult, testResults)
   }
+
 }
diff --git a/src/main/scala/io/viash/cli/CLIConf.scala b/src/main/scala/io/viash/cli/CLIConf.scala
index 950d9b1b5..f6865750e 100644
--- a/src/main/scala/io/viash/cli/CLIConf.scala
+++ b/src/main/scala/io/viash/cli/CLIConf.scala
@@ -238,14 +238,26 @@ class CLIConf(arguments: Seq[String]) extends ScallopConf(arguments) with Loggin
       "viash test",
       "Test the component using the tests defined in the viash config file.",
       "viash test config.vsh.yaml [-p docker] [-k true/false] [--setup cachedbuild]")
-    
+
     val setup = registerOpt[String](
       name = "setup",
       short = Some('s'),
       default = None,
       descr = "Which @[setup strategy](docker_setup_strategy) for creating the container to use [Docker Platform only]."
     )
-    
+    val dryRun = registerOpt[Boolean](
+      name= "dry_run",
+      default = Some(false),
+      descr = "Only generate the test script, do not run the test.",
+      hidden = true
+    )
+    val deterministicWorkingDirectory = registerOpt[String](
+      name = "deterministic_working_directory",
+      default = None,
+      descr = "Name of the working directory in the temporary directory. If not set, the working directory name will be a partially randomized name.",
+      hidden = true
+    )
+
     footer(
       s"""
          |The temporary directory can be altered by setting the VIASH_TEMP directory. Example:
@@ -336,6 +348,18 @@ class CLIConf(arguments: Seq[String]) extends ScallopConf(arguments) with Loggin
         default = Some(false),
         descr = "Append to tsv instead of overwrite"
       )
+      val dryRun = registerOpt[Boolean](
+        name= "dry_run",
+        default = Some(false),
+        descr = "Only generate the test scripts, do not run them.",
+        hidden = true
+      )
+      val deterministicWorkingDirectory = registerOpt[String](
+        name = "deterministic_working_directory",
+        default = None,
+        descr = "Name of the working directory in the temporary directory. If not set, the working directory name will be a partially randomized name.",
+        hidden = true
+      )
     }
 
     val list = new DocumentedSubcommand("list") with ViashNs with ViashLogger {
diff --git a/src/main/scala/io/viash/config/Config.scala b/src/main/scala/io/viash/config/Config.scala
index 3a474c73b..39dc8640e 100644
--- a/src/main/scala/io/viash/config/Config.scala
+++ b/src/main/scala/io/viash/config/Config.scala
@@ -24,6 +24,7 @@ import io.viash.helpers.{Git, GitInfo, IO, Logging}
 import io.viash.helpers.circe._
 import io.viash.helpers.status._
 import io.viash.helpers.Yaml
+import io.viash.ViashNamespace.targetOutputPath
 
 import java.net.URI
 import io.viash.functionality.resources._
@@ -365,6 +366,16 @@ object Config extends Logging {
 
     val allConfigs = allConfigsWithStdOutErr.collect({ case Left((config, _, _)) if config.functionality.isEnabled => config })
 
+    // Verify that all configs except the disabled ones are unique
+    // Even configs disabled by the query should be unique as they might be picked up as a dependency
+    // Only allowed exception are configs where the status is set to disabled
+    val uniqueConfigs = allConfigs.groupBy(c => targetOutputPath("", "", c))
+    val duplicateConfigs = uniqueConfigs.filter(_._2.size > 1)
+    if (duplicateConfigs.nonEmpty) {
+      val duplicateNames = duplicateConfigs.keys.map(_.dropWhile(_ == '/')).toSeq.sorted.mkString(", ")
+      throw new RuntimeException(s"Duplicate component name${ if (duplicateConfigs.size == 1) "" else "s" } found: $duplicateNames")
+    }
+
     (filteredConfigs, allConfigs)
   }
 }
diff --git a/src/main/scala/io/viash/functionality/Functionality.scala b/src/main/scala/io/viash/functionality/Functionality.scala
index eaf657381..790af8b53 100644
--- a/src/main/scala/io/viash/functionality/Functionality.scala
+++ b/src/main/scala/io/viash/functionality/Functionality.scala
@@ -372,9 +372,10 @@ case class Functionality(
     }
   def mainCode: Option[String] = mainScript.flatMap(_.read)
   // provide function to use resources.tail but that allows resources to be an empty list
+  // If mainScript ends up being None because the first resource isn't a script, return the whole list
   def additionalResources = resources match {
-    case _ :: tail => tail
-    case _ => List.empty[Resource]
+    case head :: tail if head.isInstanceOf[Script] => tail
+    case list => list
   }
 
   def isEnabled: Boolean = status != Status.Disabled
diff --git a/src/main/scala/io/viash/functionality/arguments/FileArgument.scala b/src/main/scala/io/viash/functionality/arguments/FileArgument.scala
index 1a917896a..bdb71471b 100644
--- a/src/main/scala/io/viash/functionality/arguments/FileArgument.scala
+++ b/src/main/scala/io/viash/functionality/arguments/FileArgument.scala
@@ -121,7 +121,21 @@ case class FileArgument(
   @default("Input")
   direction: Direction = Input,
 
-  @description("Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default.")
+  @description(
+    """Allow for multiple values (`false` by default).
+      |
+      |For input arguments, this will be treated as a list of values. For example, values
+      |can be passed using the delimiter `--foo=1:2:3` or by providing the same argument 
+      |multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the 
+      |[`multiple_sep`](#multiple_sep) property.
+      |
+      |For output file arguments, the passed value needs to contain a wildcard. For example,
+      |`--foo 'foo_*.txt'` will be treated as a list of files that match the pattern. Note that in Bash,
+      | the wildcard will need to be in quotes (`"foo_*.txt"` or `'foo_*.txt'`) or else Bash will
+      | automatically attempt to expand the expression.
+      |
+      |Other output arguments (e.g. integer, double, ...) are not supported yet.
+      |""".stripMargin)
   @example(
     """- name: --my_files
       |  type: file
diff --git a/src/main/scala/io/viash/functionality/dependencies/Repository.scala b/src/main/scala/io/viash/functionality/dependencies/Repository.scala
index 21d7e7741..489455243 100644
--- a/src/main/scala/io/viash/functionality/dependencies/Repository.scala
+++ b/src/main/scala/io/viash/functionality/dependencies/Repository.scala
@@ -35,7 +35,7 @@ import java.nio.file.Files
   """repositories:
     |  - name: openpipelines-bio
     |    type: github
-    |    uri: openpipelines-bio/modules
+    |    repo: openpipelines-bio/modules
     |    tag: 0.3.0
     |""".stripMargin,
     "yaml")
diff --git a/src/main/scala/io/viash/helpers/DependencyResolver.scala b/src/main/scala/io/viash/helpers/DependencyResolver.scala
index 24659f18c..389b740a2 100644
--- a/src/main/scala/io/viash/helpers/DependencyResolver.scala
+++ b/src/main/scala/io/viash/helpers/DependencyResolver.scala
@@ -156,7 +156,7 @@ object DependencyResolver {
             case "nextflow" => "main.nf"
             case _ => c.functionality.name
           }
-          Paths.get(ViashNamespace.targetOutputPath("", pid, c.functionality.namespace, c.functionality.name), executableName).toString()
+          Paths.get(ViashNamespace.targetOutputPath("", pid, c), executableName).toString()
       }
       val info = c.info.get.copy(
         executable = executable
diff --git a/src/main/scala/io/viash/helpers/IO.scala b/src/main/scala/io/viash/helpers/IO.scala
index 4b2f0d7a1..42b8d3579 100644
--- a/src/main/scala/io/viash/helpers/IO.scala
+++ b/src/main/scala/io/viash/helpers/IO.scala
@@ -55,12 +55,26 @@ object IO extends Logging {
    *
    * @param name the name of the temporary directory
    * @param parentTempPath the optional parent directory for the temporary directory
+   * @param addRandomized enable randomization of the temporary directory name
    * @return the temporary directory path
    */
-  def makeTemp(name: String, parentTempPath: Option[Path] = None): Path = {
+  def makeTemp(name: String, parentTempPath: Option[Path] = None, addRandomized: Boolean = true): Path = {
     val workTempDir = parentTempPath.getOrElse(this.tempDir)
     if (!Files.exists(workTempDir)) Files.createDirectories(workTempDir)
-    val temp = Files.createTempDirectory(workTempDir, name)
+    val temp = addRandomized match {
+      case true => Files.createTempDirectory(workTempDir, name)
+      case false => {
+        val temp = workTempDir.resolve(name)
+        val tempFile = temp.toFile()
+        if (tempFile.exists() && !tempFile.isDirectory()) {
+          throw new RuntimeException(s"Temporary directory $temp already exists as a file.")
+        }
+        if (tempFile.exists() && tempFile.isDirectory() && tempFile.list().length > 0 ){
+          throw new RuntimeException(s"Temporary directory $temp already exists and is not empty.")
+        }
+        temp
+      }
+    }
     Files.createDirectories(temp)
     temp
   }
diff --git a/src/main/scala/io/viash/platforms/DockerPlatform.scala b/src/main/scala/io/viash/platforms/DockerPlatform.scala
index 75c3bd8cc..5a8d51893 100644
--- a/src/main/scala/io/viash/platforms/DockerPlatform.scala
+++ b/src/main/scala/io/viash/platforms/DockerPlatform.scala
@@ -122,11 +122,11 @@ case class DockerPlatform(
       +| `ifneedbebuild` |  Build the image if it does not exist locally.
       +| `ifneedbecachedbuild` | Build the image with caching enabled if it does not exist locally, with caching enabled.
       +| `alwayspull` / `pull` / `p` |  Try to pull the container from [Docker Hub](https://hub.docker.com) or the @[specified docker registry](docker_registry).
-      +| `alwayspullelsebuild` / `pullelsebuild` |  Try to pull the image from a registry and build it if it doesn't exist.
-      +| `alwayspullelsecachedbuild` / `pullelsecachedbuild` |  Try to pull the image from a registry and build it with caching if it doesn't exist.
+      +| `alwayspullelsebuild` / `pullelsebuild` |  Try to pull the image from a registry and build it if it does not exist.
+      +| `alwayspullelsecachedbuild` / `pullelsecachedbuild` |  Try to pull the image from a registry and build it with caching if it does not exist.
       +| `ifneedbepull` |  If the image does not exist locally, pull the image.
-      +| `ifneedbepullelsebuild` |  If the image does not exist locally, pull the image. If the image does exist, build it.
-      +| `ifneedbepullelsecachedbuild` | If the image does not exist locally, pull the image. If the image does exist, build it with caching enabled.
+      +| `ifneedbepullelsebuild` |  Do nothing if the image exists locally. Else, try to pull the image from a registry. Otherwise build the image from scratch.
+      +| `ifneedbepullelsecachedbuild` | Do nothing if the image exists locally. Else, try to pull the image from a registry. Otherwise build the image with caching enabled.
       +| `push` | Push the container to [Docker Hub](https://hub.docker.com)  or the @[specified docker registry](docker_registry).
       +| `pushifnotpresent` | Push the container to [Docker Hub](https://hub.docker.com) or the @[specified docker registry](docker_registry) if the @[tag](docker_tag) does not exist yet.
       +| `donothing` / `meh` | Do not build or pull anything.
@@ -476,7 +476,7 @@ case class DockerPlatform(
     val preRun =
       if (resolve_volume == Automatic) {
         val detectMounts = args.flatMap {
-          case arg: FileArgument if arg.multiple =>
+          case arg: FileArgument if arg.multiple && arg.direction == Input =>
             // resolve arguments with multiplicity different from singular args
             val viash_temp = "VIASH_TEST_" + arg.plainName.toUpperCase()
             val chownIfOutput = if (arg.direction == Output) "\n    VIASH_CHOWN_VARS+=( \"$var\" )" else ""
@@ -611,7 +611,7 @@ case class DockerPlatform(
            |function ViashPerformChown {
            |  if (( $${#VIASH_CHOWN_VARS[@]} )); then
            |    set +e
-           |    eval docker run --entrypoint=chown $dockerArgs$volExtraParams $fullImageID "$$(id -u):$$(id -g)" --silent --recursive $${VIASH_CHOWN_VARS[@]}
+           |    eval docker run --entrypoint=bash $dockerArgs$volExtraParams $fullImageID -c "'chown $$(id -u):$$(id -g) --silent --recursive $${VIASH_CHOWN_VARS[@]}'"
            |    set -e
            |  fi
            |}
diff --git a/src/main/scala/io/viash/platforms/NextflowPlatform.scala b/src/main/scala/io/viash/platforms/NextflowPlatform.scala
index 2f9ba1acc..a4d171904 100644
--- a/src/main/scala/io/viash/platforms/NextflowPlatform.scala
+++ b/src/main/scala/io/viash/platforms/NextflowPlatform.scala
@@ -245,6 +245,7 @@ case class NextflowPlatform(
           NextflowHelper.vdsl3Helper
     }
 
+    // TODO: might need to change resources_dir to just moduleDir
     NextflowHelper.generateHeader(config) + "\n\n" +
       NextflowHelper.workflowHelper +
       s"""
@@ -255,7 +256,7 @@ case class NextflowPlatform(
       |
       |// create meta object
       |meta = [
-      |  "resources_dir": moduleDir.toRealPath().normalize(),
+      |  "resources_dir": moduleDir,
       |  "config": ${NextflowHelper.generateConfigStr(config)}
       |]
       |
@@ -277,7 +278,6 @@ case class NextflowPlatform(
       |// anonymous workflow for running this module as a standalone
       |workflow {
       |  // add id argument if it's not already in the config
-      |  // TODO: deep copy
       |  def newConfig = deepClone(meta.config)
       |  def newParams = deepClone(params)
       |
diff --git a/src/main/scala/io/viash/platforms/nextflow/NextflowHelper.scala b/src/main/scala/io/viash/platforms/nextflow/NextflowHelper.scala
index d025c2a8a..f7ce66e1e 100644
--- a/src/main/scala/io/viash/platforms/nextflow/NextflowHelper.scala
+++ b/src/main/scala/io/viash/platforms/nextflow/NextflowHelper.scala
@@ -221,7 +221,7 @@ object NextflowHelper {
 
   def renderDependencies(config: Config): String = {
     // TODO ideally we'd already have 'thisPath' precalculated but until that day, calculate it here
-    val thisPath = Paths.get(ViashNamespace.targetOutputPath("", "invalid_platform_name", config.functionality.namespace, config.functionality.name))
+    val thisPath = Paths.get(ViashNamespace.targetOutputPath("", "invalid_platform_name", config))
 
     val depStrs = config.functionality.dependencies.map{ dep =>
       NextflowHelper.renderInclude(dep, thisPath)
diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index 1de46cbcd..7a5f24c7d 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -231,7 +231,7 @@ object BashWrapper {
     val localDependenciesStrings = localDependencies.map{ d =>
       // relativize the path of the main component to the local dependency
       // TODO ideally we'd already have 'thisPath' precalculated but until that day, calculate it here
-      val thisPath = ViashNamespace.targetOutputPath("", "invalid_platform_name", config.functionality.namespace, config.functionality.name)
+      val thisPath = ViashNamespace.targetOutputPath("", "invalid_platform_name", config)
       val relativePath = Paths.get(thisPath).relativize(Paths.get(d.configInfo.getOrElse("executable", "")))
       s"${d.VIASH_DEP}=\"$$VIASH_META_RESOURCES_DIR/$relativePath\""
     }
@@ -361,7 +361,12 @@ object BashWrapper {
 
         (part1 :: moreParts).mkString("\n")
       case param =>
-        val multisep = if (param.multiple) Some(param.multiple_sep) else None
+        val multisep =
+          if (param.multiple && param.direction == Input) {
+            Some(param.multiple_sep)
+          } else {
+            None
+          }
 
         // params of the form --param ...
         val part1 = param.flags match {
@@ -389,7 +394,7 @@ object BashWrapper {
       } else {
         "\n# storing leftover values in positionals\n" +
         positionals.map { param =>
-          if (param.multiple) {
+          if (param.multiple && param.direction == Input) {
             s"""while [[ $$# -gt 0 ]]; do
               |  ${store("positionalArg", param.VIASH_PAR, "\"$1\"", Some(param.multiple_sep)).mkString("\n  ")}
               |  shift 1
@@ -456,7 +461,12 @@ object BashWrapper {
       } else {
         "\n# check whether required files exist\n" +
           files.map { param =>
-            if (param.multiple) {
+            if (!param.multiple) {
+              s"""if [ ! -z "$$${param.VIASH_PAR}" ] && [ ! -e "$$${param.VIASH_PAR}" ]; then
+                 |  ViashError "$direction file '$$${param.VIASH_PAR}' does not exist."
+                 |  exit 1
+                 |fi""".stripMargin
+            } else if (direction == Input) {
               s"""if [ ! -z "$$${param.VIASH_PAR}" ]; then
                  |  IFS='${Bash.escapeString(param.multiple_sep, quote = true)}'
                  |  set -f
@@ -469,11 +479,11 @@ object BashWrapper {
                  |  done
                  |  set +f
                  |fi""".stripMargin
-            } else {
-              s"""if [ ! -z "$$${param.VIASH_PAR}" ] && [ ! -e "$$${param.VIASH_PAR}" ]; then
-                |  ViashError "$direction file '$$${param.VIASH_PAR}' does not exist."
-                |  exit 1
-                |fi""".stripMargin
+            } else { // multiple: true, direction: output expects arguments in the form of "output_*.txt"
+              s"""if [ ! -z "$$${param.VIASH_PAR}" ] && ! compgen -G "$$${param.VIASH_PAR}" > /dev/null; then
+                 |  ViashError "$direction file '$$${param.VIASH_PAR}' does not exist."
+                 |  exit 1
+                 |fi""".stripMargin
             }
           }.mkString("\n")
       }
@@ -492,7 +502,7 @@ object BashWrapper {
       } else {
         "\n# create parent directories of output files, if so desired\n" +
           createParentFiles.map { param =>
-            if (param.multiple) {
+            if (param.multiple && param.direction == Input) {
               s"""if [ ! -z "$$${param.VIASH_PAR}" ]; then
                  |  IFS='${Bash.escapeString(param.multiple_sep, quote = true)}'
                  |  set -f
@@ -515,7 +525,8 @@ object BashWrapper {
     // construct type checks
     def typeMinMaxCheck[T](param: Argument[T], regex: String, min: Option[T] = None, max: Option[T] = None) = {
       val typeWithArticle = param match {
-        case i: IntegerArgument => "an " + param.`type`
+        case _: FileArgument if param.multiple && param.direction == Output => "a path containing a wildcard, e.g. 'output_*.txt'"
+        case _: IntegerArgument => "an " + param.`type`
         case _ => "a " + param.`type`
       }
 
@@ -583,7 +594,7 @@ object BashWrapper {
       }
 
       param match {
-        case param if param.multiple =>
+        case param if param.multiple && param.direction == Input =>
           val checkStart = 
             s"""if [ -n "$$${param.VIASH_PAR}" ]; then
                |  IFS='${Bash.escapeString(param.multiple_sep, quote = true)}'
@@ -624,17 +635,18 @@ object BashWrapper {
                 Some(typeMinMaxCheck(dO, "^[-+]?(\\.[0-9]+|[0-9]+(\\.[0-9]*)?)([eE][-+]?[0-9]+)?$", dO.min, dO.max))
               case bo: BooleanArgumentBase =>
                 Some(typeMinMaxCheck(bo, "^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$"))
+              case fo: FileArgument if fo.multiple && fo.direction == Output =>
+                Some(typeMinMaxCheck(fo, "\\*"))
               case _ => None
             }           
           }.mkString("\n")
       }
 
-
     def checkChoices[T](param: Argument[T], allowedChoices: List[T]) = {
       val allowedChoicesString = allowedChoices.mkString(param.multiple_sep.toString)
 
       param match {
-        case _ if param.multiple =>
+        case _ if param.multiple && param.direction == Input =>
           s"""if [ ! -z "$$${param.VIASH_PAR}" ]; then
              |  ${param.VIASH_PAR}_CHOICES=("$allowedChoicesString")
              |  IFS='${Bash.escapeString(param.multiple_sep, quote = true)}'
@@ -777,7 +789,7 @@ object BashWrapper {
       case param =>
         val flag = if (param.flags == "") "" else " " + param.name
 
-        if (param.multiple) {
+        if (param.multiple && param.direction == Input) {
           s"""
              |if [ ! -z "$$${param.VIASH_PAR}" ]; then
              |  IFS='${Bash.escapeString(param.multiple_sep, quote = true)}'
diff --git a/src/test/resources/testbash/code.sh b/src/test/resources/testbash/code.sh
index 0b8d8468c..d341a11e4 100755
--- a/src/test/resources/testbash/code.sh
+++ b/src/test/resources/testbash/code.sh
@@ -9,6 +9,7 @@ par_truth="true"
 par_falsehood="false"
 par_reality=""
 par_output="output.txt"
+par_multiple_output="output*.txt"
 par_log="log.txt"
 par_optional="help"
 par_optional_with_default="me"
@@ -55,5 +56,17 @@ output "optional: |$par_optional|"
 output "optional_with_default: |$par_optional_with_default|"
 output "multiple: |$par_multiple|"
 output "multiple_pos: |$par_multiple_pos|"
-
+output "multiple_output: |$par_multiple_output|"
 output "meta_resources_dir: |$meta_resources_dir|"
+
+multiple_output_i=0
+if [ ! -z "$par_multiple_output" ]; then
+  multiple_output_file=$(echo $par_multiple_output | sed "s/\*/$multiple_output_i/")
+  cp "$par_input" "$multiple_output_file"
+  multiple_output_i=$((multiple_output_i+1))
+
+  multiple_output_file=$(echo $par_multiple_output | sed "s/\*/$multiple_output_i/")
+  cp "$par_input" "$multiple_output_file"
+  multiple_output_i=$((multiple_output_i+1))
+fi
+
diff --git a/src/test/resources/testbash/config.vsh.yaml b/src/test/resources/testbash/config.vsh.yaml
index c29fb6c13..767ce505a 100755
--- a/src/test/resources/testbash/config.vsh.yaml
+++ b/src/test/resources/testbash/config.vsh.yaml
@@ -72,6 +72,10 @@ functionality:
         - name: "multiple_pos"
           type: string
           multiple: true
+        - name: "--multiple_output"
+          type: file
+          multiple: true
+          direction: output
   resources:
     - type: bash_script
       path: ./code.sh
diff --git a/src/test/resources/testbash/docker_options/code_multiple_output.sh b/src/test/resources/testbash/docker_options/code_multiple_output.sh
index 02be284e3..656dbb728 100755
--- a/src/test/resources/testbash/docker_options/code_multiple_output.sh
+++ b/src/test/resources/testbash/docker_options/code_multiple_output.sh
@@ -9,60 +9,17 @@ par_truth="true"
 par_falsehood="false"
 par_reality=""
 par_output="output.txt"
+par_multiple_output="output_*.txt"
 par_log="log.txt"
 par_optional="help"
 par_optional_with_default="me"
 meta_resources_dir="."
 # VIASH END
 
-set -e
+par_out_1=`echo "$par_multiple_output" | sed 's/\*/1/g'`
+par_out_2=`echo "$par_multiple_output" | sed 's/\*/2/g'`
+par_out_3=`echo "$par_multiple_output" | sed 's/\*/3/g'`
 
-function log {
-  if [ -z "$par_log" ]; then
-    echo "$@"
-  else
-    echo "$@" >> $par_log
-  fi
-}
-function output {
-  if [ -z "$par_output" ]; then
-    echo "$@"
-  else
-    echo "$@" >> $par_output
-
-    if [ ! -z "$par_output_pos" ]; then
-      IFS=":"
-      for var in $par_output_pos; do
-        unset IFS
-        echo "$@" >> $var
-      done
-    fi
-
-  fi
-}
-
-log "INFO: Parsed input arguments."
-
-if [ -z "$par_output" ]; then
-  log "INFO: Printing output to console"
-else
-  log "INFO: Writing output to file"
-fi
-
-output "input: |$par_input|"
-output "real_number: |$par_real_number|"
-output "whole_number: |$par_whole_number|"
-output "s: |$par_s|"
-output "truth: |$par_truth|"
-output "falsehood: |$par_falsehood|"
-output "reality: |$par_reality|"
-output "output: |$par_output|"
-output "log: |$par_log|"
-output "optional: |$par_optional|"
-output "optional_with_default: |$par_optional_with_default|"
-output "meta_resources_dir: |$meta_resources_dir|"
-INPUT=`head -1 "$par_input"`
-output "head of input: |$INPUT|"
-RESOURCE=`head -1 "$meta_resources_dir/resource1.txt"`
-output "head of resource1: |$RESOURCE|"
-output "output_pos: |$par_output_pos|"
+echo "input: |$par_input|" > $par_out_1
+echo "real_number: |$par_real_number|" > $par_out_2
+echo "whole_number: |$par_whole_number|" > $par_out_3
diff --git a/src/test/resources/testbash/tests/check_outputs.sh b/src/test/resources/testbash/tests/check_outputs.sh
index ece0cd0c6..a146e3543 100755
--- a/src/test/resources/testbash/tests/check_outputs.sh
+++ b/src/test/resources/testbash/tests/check_outputs.sh
@@ -14,7 +14,8 @@ echo ">>> Checking whether output is correct"
   --output ./output.txt --log ./log.txt \
   --multiple one --multiple=two \
   e f \
-  --long_number 112589990684262400
+  --long_number 112589990684262400 \
+  --multiple_output './output_*.txt'
 
 [[ ! -f output.txt ]] && echo "Output file could not be found!" && exit 1
 grep -q 'input: |NOTICE|' output.txt
@@ -31,5 +32,6 @@ grep -q 'optional: |foo|' output.txt
 grep -q 'optional_with_default: |bar|' output.txt
 grep -q 'multiple: |one:two|' output.txt
 grep -q 'multiple_pos: |a:b:c:d:e:f|' output.txt
+grep -q 'multiple_output: |.*/output_\*.txt|' output.txt
 
 echo ">>> Test finished successfully"
diff --git a/src/test/resources/testnextflowvdsl3/src/multiple_output/config.vsh.yaml b/src/test/resources/testnextflowvdsl3/src/multiple_output/config.vsh.yaml
new file mode 100644
index 000000000..94d0eeec5
--- /dev/null
+++ b/src/test/resources/testnextflowvdsl3/src/multiple_output/config.vsh.yaml
@@ -0,0 +1,24 @@
+functionality:
+  name: multiple_output
+  arguments:
+    - name: "--input"
+      type: file
+      multiple: true
+      required: true
+      example: input.txt
+      multiple_sep: ";"
+    - name: "--output"
+      type: file
+      required: true
+      direction: output
+      multiple: true
+      multiple_sep: ";"
+      example: output_*.txt
+  resources:
+    - type: bash_script
+      path: script.sh
+platforms:
+  - type: native
+  - type: docker
+    image: nextflow/bash:latest
+  - type: nextflow
diff --git a/src/test/resources/testnextflowvdsl3/src/multiple_output/script.sh b/src/test/resources/testnextflowvdsl3/src/multiple_output/script.sh
new file mode 100644
index 000000000..c9ffcea7a
--- /dev/null
+++ b/src/test/resources/testnextflowvdsl3/src/multiple_output/script.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+## VIASH START
+par_input='resources/lines3.txt;resources/lines5.txt'
+par_output='output_*.txt'
+## VIASH END
+
+output_i=0
+
+if [ ! -z "$par_input" ]; then
+  IFS=";"
+  for var in $par_input; do
+    unset IFS
+    output=$(echo "$par_output" | sed "s/\*/$output_i/g")
+    cp "$var" "$output"
+    output_i=$((output_i+1))
+  done
+fi
diff --git a/src/test/resources/testnextflowvdsl3/src/test_wfs/concurrency/main.nf b/src/test/resources/testnextflowvdsl3/src/test_wfs/concurrency/main.nf
index d16051213..e3a649ad2 100644
--- a/src/test/resources/testnextflowvdsl3/src/test_wfs/concurrency/main.nf
+++ b/src/test/resources/testnextflowvdsl3/src/test_wfs/concurrency/main.nf
@@ -6,7 +6,7 @@ workflow base {
   ch = Channel.fromList(0..1000)
     | map { num ->
       // create temporary file
-      file = tempFile()
+      def file = tempFile()
       file.write("num: $num")
 
       ["num$num", [ num: num, file: file ]]
diff --git a/src/test/resources/testnextflowvdsl3/src/test_wfs/nested/main.nf b/src/test/resources/testnextflowvdsl3/src/test_wfs/nested/main.nf
index 2ba19788d..96e810b5d 100644
--- a/src/test/resources/testnextflowvdsl3/src/test_wfs/nested/main.nf
+++ b/src/test/resources/testnextflowvdsl3/src/test_wfs/nested/main.nf
@@ -6,7 +6,7 @@ workflow base {
   ch = Channel.fromList(0..1000)
     | map { num ->
       // create temporary file
-      file = tempFile()
+      def file = tempFile()
       file.write("num: $num")
 
       ["num$num", [ file: file ], ["num": num]]
diff --git a/src/test/resources/testnextflowvdsl3/src/test_wfs/runeach/main.nf b/src/test/resources/testnextflowvdsl3/src/test_wfs/runeach/main.nf
index ce752a546..9eca5abb4 100644
--- a/src/test/resources/testnextflowvdsl3/src/test_wfs/runeach/main.nf
+++ b/src/test/resources/testnextflowvdsl3/src/test_wfs/runeach/main.nf
@@ -15,7 +15,7 @@ workflow base {
   
     | map { num ->
       // create temporary file
-      file = tempFile()
+      def file = tempFile()
       file.write("num: $num")
 
       ["num$num", [ num: num, file: file ]]
@@ -26,7 +26,6 @@ workflow base {
       toState: ["step1_output": "output"]
     )
 
-
     | step1.run(
       key: "step1bis",
       fromState: { id, state ->
diff --git a/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerChown.scala b/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerChown.scala
index a5a1f3152..cdcb27fb7 100644
--- a/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerChown.scala
+++ b/src/test/scala/io/viash/auxiliary/MainBuildAuxiliaryDockerChown.scala
@@ -30,10 +30,7 @@ class MainBuildAuxiliaryDockerChown extends AnyFunSuite with BeforeAndAfterAll w
   )
 
   val multipleOutputsMods = List(
-    """del(.functionality.argument_groups[.name == "Arguments"].arguments[.name == "--multiple"])""",
-    """del(.functionality.argument_groups[.name == "Arguments"].arguments[.name == "multiple_pos"])""",
-    """.functionality.argument_groups[.name == "Arguments"].arguments[.name == "--output"].multiple := true""",
-    """.functionality.argument_groups[.name == "Arguments"].arguments += {name: "output_pos", type: "file", direction: "output", multiple: true}""",
+    """.functionality.argument_groups[.name == "Arguments"].arguments[.name == "--output"].required := false""",
     """.functionality.resources[.type == "bash_script"].path := "docker_options/code_multiple_output.sh"""",
   )
 
@@ -61,14 +58,12 @@ class MainBuildAuxiliaryDockerChown extends AnyFunSuite with BeforeAndAfterAll w
     assert(localExecutable.canExecute)
 
     // run the script
-    val output = Paths.get(tempFolStr, "output_" + dockerId + ".txt").toFile
-    val output2 = Paths.get(tempFolStr, "output_" + dockerId +"_2.txt").toFile
-    val output3 = Paths.get(tempFolStr, "output_" + dockerId +"_3.txt").toFile
+    val pattern = f"$tempFolStr/output_${dockerId}_*.txt"
 
     val outputParams = amount match {
-      case 1 => Seq("--output", output.getPath)
-      case 2 => Seq("--output", output.getPath, "--output2", output2.getPath)
-      case 3 => Seq("--output", output.getPath, output2.getPath, output3.getPath)
+      case 1 => Seq("--output", pattern.replace("*", "1"))
+      case 2 => Seq("--output", pattern.replace("*", "1"), "--output2", pattern.replace("*", "2"))
+      case 3 => Seq("--multiple_output", pattern)
     }
 
     Exec.run(
@@ -81,9 +76,12 @@ class MainBuildAuxiliaryDockerChown extends AnyFunSuite with BeforeAndAfterAll w
       ) ++ outputParams
     )
 
-    val outputList = List(output, output2, output3).take(amount)
-    outputList.foreach(output => assert(output.exists()))
-    outputList.map(file => Files.getOwner(file.toPath).toString)
+    // find files based on the pattern
+    import scala.jdk.CollectionConverters._
+    val foundFiles = Files.list(temporaryFolder).iterator().asScala.toList
+    val outputFiles = foundFiles.filter(_.toString.matches(pattern.replace("*", ".*")))
+    assert(outputFiles.length == amount, s"Expected $amount files, got ${outputFiles.length}.\nDirectory contents: ${foundFiles.mkString(", ")}")
+    outputFiles.map(file => Files.getOwner(file).toString)
   }
 
   test("Test default behaviour when chown is not specified", DockerTest) {
diff --git a/src/test/scala/io/viash/e2e/build/DockerSuite.scala b/src/test/scala/io/viash/e2e/build/DockerSuite.scala
index bb05704e2..d1402ef6d 100644
--- a/src/test/scala/io/viash/e2e/build/DockerSuite.scala
+++ b/src/test/scala/io/viash/e2e/build/DockerSuite.scala
@@ -111,7 +111,7 @@ class DockerSuite extends AnyFunSuite with BeforeAndAfterAll {
       assert(outputLines.contains("""optional_with_default: |bar|"""))
       assert(outputLines.contains("""multiple: |foo:bar|"""))
       assert(outputLines.contains("""multiple_pos: |a:b:c:d:e:f|"""))
-      val regex = s"""meta_resources_dir: \\|.*${temporaryFolder}/\\|""".r
+      val regex = s"""meta_resources_dir: \\|.*${temporaryFolder}\\|""".r
       assert(regex.findFirstIn(outputLines).isDefined)
     } finally {
       outputSrc.close()
@@ -148,7 +148,7 @@ class DockerSuite extends AnyFunSuite with BeforeAndAfterAll {
     assert(stdout.contains("""optional_with_default: |The default value.|"""))
     assert(stdout.contains("""multiple: ||"""))
     assert(stdout.contains("""multiple_pos: ||"""))
-    val regex = s"""meta_resources_dir: \\|/viash_automount.*$temporaryFolder/\\|""".r
+    val regex = s"""meta_resources_dir: \\|/viash_automount.*$temporaryFolder\\|""".r
     assert(regex.findFirstIn(stdout).isDefined)
 
     assert(stdout.contains("INFO: Parsed input arguments"))
@@ -157,4 +157,4 @@ class DockerSuite extends AnyFunSuite with BeforeAndAfterAll {
   override def afterAll(): Unit = {
     IO.deleteRecursively(temporaryFolder)
   }
-}
\ No newline at end of file
+}
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 269d7ffcd..8c3eabdf1 100644
--- a/src/test/scala/io/viash/e2e/ns_build/MainNSBuildNativeSuite.scala
+++ b/src/test/scala/io/viash/e2e/ns_build/MainNSBuildNativeSuite.scala
@@ -109,6 +109,96 @@ class MainNSBuildNativeSuite extends AnyFunSuite with BeforeAndAfterAll{
     }
   }
 
+  test("Check uniqueness of component names, same name, different namespace") {
+    val compStr =
+      """functionality:
+        |  name: comp
+        |  namespace: %s
+        |""".stripMargin
+    val tempSrcDir = IO.makeTemp("viash_ns_build_check_uniqueness_src")
+    IO.write(compStr.format("ns1"), tempSrcDir.resolve("config1.vsh.yaml"))
+    IO.write(compStr.format("ns2"), tempSrcDir.resolve("config2.vsh.yaml"))
+
+    val tempTargetDir = IO.makeTemp("viash_ns_build_check_uniqueness_target")
+
+    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+      "ns", "build",
+        "-s", tempSrcDir.toString(),
+        "-t", tempTargetDir.toString()
+      )
+
+    assert(exitCode == 0)
+    assert(stderr.contains("All 2 configs built successfully"))
+  }
+
+  test("Check uniqueness of component names, different name, same namespace") {
+    val compStr =
+      """functionality:
+        |  name: %s
+        |  namespace: ns
+        |""".stripMargin
+    val tempSrcDir = IO.makeTemp("viash_ns_build_check_uniqueness_src")
+    IO.write(compStr.format("comp1"), tempSrcDir.resolve("config1.vsh.yaml"))
+    IO.write(compStr.format("comp2"), tempSrcDir.resolve("config2.vsh.yaml"))
+
+    val tempTargetDir = IO.makeTemp("viash_ns_build_check_uniqueness_target")
+
+    val (stdout, stderr, exitCode) = TestHelper.testMainWithStdErr(
+      "ns", "build",
+        "-s", tempSrcDir.toString(),
+        "-t", tempTargetDir.toString()
+      )
+
+    assert(exitCode == 0)
+    assert(stderr.contains("All 2 configs built successfully"))
+  }
+
+  test("Check uniqueness of component names, same name, same namespace") {
+    val compStr =
+      """functionality:
+        |  name: %s
+        |  namespace: ns
+        |""".stripMargin
+    val tempSrcDir = IO.makeTemp("viash_ns_build_check_uniqueness_src")
+    IO.write(compStr.format("comp"), tempSrcDir.resolve("config1.vsh.yaml"))
+    IO.write(compStr.format("comp"), tempSrcDir.resolve("config2.vsh.yaml"))
+
+    val tempTargetDir = IO.makeTemp("viash_ns_build_check_uniqueness_target")
+
+    val testOutput = TestHelper.testMainException2[RuntimeException](
+      "ns", "build",
+        "-s", tempSrcDir.toString(),
+        "-t", tempTargetDir.toString()
+      )
+
+    assert(!testOutput.error.contains("All 2 configs built successfully"))
+    assert(testOutput.exceptionText.contains("Duplicate component name found: ns/comp"))
+  }
+
+  test("Check uniqueness of component names, same name, same namespace - multiple duplicates") {
+    val compStr =
+      """functionality:
+        |  name: %s
+        |  namespace: ns
+        |""".stripMargin
+    val tempSrcDir = IO.makeTemp("viash_ns_build_check_uniqueness_src")
+    IO.write(compStr.format("comp1"), tempSrcDir.resolve("config1.vsh.yaml"))
+    IO.write(compStr.format("comp1"), tempSrcDir.resolve("config2.vsh.yaml"))
+    IO.write(compStr.format("comp2"), tempSrcDir.resolve("config3.vsh.yaml"))
+    IO.write(compStr.format("comp2"), tempSrcDir.resolve("config4.vsh.yaml"))
+
+    val tempTargetDir = IO.makeTemp("viash_ns_build_check_uniqueness_target")
+
+    val testOutput = TestHelper.testMainException2[RuntimeException](
+      "ns", "build",
+        "-s", tempSrcDir.toString(),
+        "-t", tempTargetDir.toString()
+      )
+
+    assert(!testOutput.error.contains("All 2 configs built successfully"))
+    assert(testOutput.exceptionText.contains("Duplicate component names found: ns/comp1, ns/comp2"))
+  }
+
   override def afterAll(): Unit = {
     IO.deleteRecursively(temporaryFolder)
   }
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 489ab1ec2..84a84bd31 100644
--- a/src/test/scala/io/viash/e2e/ns_test/MainNSTestNativeSuite.scala
+++ b/src/test/scala/io/viash/e2e/ns_test/MainNSTestNativeSuite.scala
@@ -96,6 +96,39 @@ class MainNSTestNativeSuite 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")
   }
+  
+  test("Check namespace test output with working dir message using --dry_run") {
+    val (stdout, stderr, _) = TestHelper.testMainWithStdErr(
+      "ns", "test",
+      "--src", nsPath,
+      "--keep", "true",
+      "--dry_run"
+    )
+
+    // Test inclusion of a header
+    val regexHeader = raw"^\s*namespace\s*functionality\s*platform\s*test_name\s*exit_code\s*duration\s*result".r
+    assert(regexHeader.findFirstIn(stdout).isDefined, s"\nRegex: ${regexHeader.toString}; text: \n${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}")
+
+    for (
+      (component, steps) <- components;
+      (step, resultPattern) <- steps
+    ) {
+      // In this mode, a test script can never return an ERROR
+      val updtResultPattern = if (resultPattern == raw"\s*1\s*\d+\s*ERROR") {
+        raw"\s*0\s*\d+\s*SUCCESS"
+      } else {
+        resultPattern
+      }
+      val regex = s"""testns\\s*$component\\s*native\\s*$step$updtResultPattern""".r
+      assert(regex.findFirstIn(stdout).isDefined, s"\nRegex: '${regex.toString}'; text: \n${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")
+  }
 
   test("Check namespace test output with tsv option") {
     val log = Paths.get(tempFolStr, "log.tsv").toFile
@@ -194,6 +227,37 @@ class MainNSTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
     }
   }
 
+  test("Check namespace test output with deterministic working directory") {
+    // create a new unique temporary folder
+    val temporaryFolder = IO.makeTemp(s"viash_${this.getClass.getName}_")
+    val tempFolStr = temporaryFolder.getFileName().toString()
+
+    val (stdout, stderr, _) = TestHelper.testMainWithStdErr(
+      "ns", "test",
+      "--src", nsPath,
+      "--deterministic_working_directory", tempFolStr
+    )
+
+    assert(stderr.contains(s"The working directory for the namespace tests is ${temporaryFolder}"))
+
+    // Test inclusion of a header
+    val regexHeader = raw"^\s*namespace\s*functionality\s*platform\s*test_name\s*exit_code\s*duration\s*result".r
+    assert(regexHeader.findFirstIn(stdout).isDefined, s"\nRegex: ${regexHeader.toString}; text: \n$stdout")
+
+    for (
+      (component, steps) <- components;
+      (step, resultPattern) <- steps
+    ) {
+      val regex = s"""testns\\s*$component\\s*native\\s*$step$resultPattern""".r
+      assert(regex.findFirstIn(stdout).isDefined, s"\nRegex: '${regex.toString}'; text: \n$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(stderr.contains("The status of the component 'ns_power' is set to deprecated."))
+  }
+
   override def afterAll(): Unit = {
     IO.deleteRecursively(temporaryFolder)
   }
diff --git a/src/test/scala/io/viash/e2e/test/MainTestNativeSuite.scala b/src/test/scala/io/viash/e2e/test/MainTestNativeSuite.scala
index 0558ccff1..76fc8b269 100644
--- a/src/test/scala/io/viash/e2e/test/MainTestNativeSuite.scala
+++ b/src/test/scala/io/viash/e2e/test/MainTestNativeSuite.scala
@@ -228,6 +228,21 @@ class MainTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
     checkTempDirAndRemove(testText, true)
   }
 
+  test("Check output in case --dry_run is specified") {
+    val testText = TestHelper.testMain(
+      "test",
+      "-p", "native",
+      "--dry_run",
+      configFile
+    )
+    assert(testText.contains("Running tests in temporary directory: "))
+    assert(testText.contains("Running dummy test script"))
+    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testText.contains("Cleaning up temporary directory"))
+
+    checkTempDirAndRemove(testText, false)
+  }
+
   test("Check output in case --keep false is specified") {
     val testText = TestHelper.testMain(
       "test",
@@ -311,6 +326,64 @@ class MainTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
     assert(testOutput.output.isEmpty)
   }
 
+  test("Check standard test output with deterministic build folder that exists but is empty") {
+    // create a new unique temporary folder
+    val temporaryFolder = IO.makeTemp(s"viash_${this.getClass.getName}_")
+    val tempFolStr = temporaryFolder.getFileName().toString()
+
+    val testText = TestHelper.testMain(
+      "test",
+      "-p", "native",
+      "--deterministic_working_directory", tempFolStr,
+      configFile
+    )
+
+    assert(testText.contains(s"Running tests in temporary directory: '${temporaryFolder}'"))
+    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testText.contains("Cleaning up temporary directory"))
+
+    checkTempDirAndRemove(testText, false, tempFolStr)
+  }
+
+  test("Check standard test output with deterministic build folder that doesn't exist yet") {
+    // create a new unique temporary folder to know what folder name to use
+    val temporaryFolder = IO.makeTemp(s"viash_${this.getClass.getName}_")
+    temporaryFolder.toFile().delete()
+    val tempFolStr = temporaryFolder.getFileName().toString()
+
+    val testText = TestHelper.testMain(
+      "test",
+      "-p", "native",
+      "--deterministic_working_directory", tempFolStr,
+      configFile
+    )
+
+    assert(testText.contains(s"Running tests in temporary directory: '${temporaryFolder}'"))
+    assert(testText.contains("SUCCESS! All 2 out of 2 test scripts succeeded!"))
+    assert(testText.contains("Cleaning up temporary directory"))
+
+    checkTempDirAndRemove(testText, false, tempFolStr)
+  }
+
+  test("Check standard test output with deterministic build folder that isn't empty") {
+    // create a new unique temporary folder to know what folder name to use
+    val temporaryFolder = IO.makeTemp(s"viash_${this.getClass.getName}_")
+    IO.write("foo", temporaryFolder.resolve("foo.txt"))
+    val tempFolStr = temporaryFolder.getFileName().toString()
+
+    val testOutput = TestHelper.testMainException2[RuntimeException](
+      "test",
+      "-p", "native",
+      "--deterministic_working_directory", tempFolStr,
+      configFile
+    )
+
+    assert(testOutput.exceptionText.contains(s"${temporaryFolder} already exists and is not empty."))
+
+    assert(testOutput.output.isEmpty())
+    assert(testOutput.error.isEmpty())
+  }
+
   /**
    * Searches the output generated by Main.main() during tests for the temporary directory name and verifies if it still exists or not.
    * If directory was expected to be present and actually is present, it will be removed.
@@ -318,7 +391,7 @@ class MainTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
    * @param expectDirectoryExists expect the directory to be present or not
    * @return
    */
-  def checkTempDirAndRemove(testText: String, expectDirectoryExists: Boolean): Unit = {
+  def checkTempDirAndRemove(testText: String, expectDirectoryExists: Boolean, testDirName: String = "viash_test_testbash"): Unit = {
     // Get temporary directory
     val FolderRegex = ".*Running tests in temporary directory: '([^']*)'.*".r
 
@@ -327,7 +400,7 @@ class MainTestNativeSuite extends AnyFunSuite with BeforeAndAfterAll {
       case _ => ""
     }
 
-    assert(tempPath.contains(s"${IO.tempDir}/viash_test_testbash"))
+    assert(tempPath.contains(s"${IO.tempDir}/$testDirName"))
 
     val tempFolder = new Directory(Paths.get(tempPath).toFile)
 
diff --git a/src/test/scala/io/viash/functionality/MainScriptTest.scala b/src/test/scala/io/viash/functionality/MainScriptTest.scala
new file mode 100644
index 000000000..ab485abcc
--- /dev/null
+++ b/src/test/scala/io/viash/functionality/MainScriptTest.scala
@@ -0,0 +1,108 @@
+package io.viash.functionality
+
+import org.scalatest.funsuite.AnyFunSuite
+import io.viash.helpers.Logger
+import io.viash.functionality.resources.{BashScript, PlainFile}
+
+class MainScriptTest extends AnyFunSuite {
+  Logger.UseColorOverride.value = Some(false)
+
+  test("Single script") {
+    val resources = List(BashScript(path = Some("foo.sh")))
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isDefined)
+    assert(mainScript.get.path == Some("foo.sh"))
+    assert(additionalResources.isEmpty)
+  }
+
+  test("Multiple scripts") {
+    val resources = List(
+      BashScript(path = Some("foo.sh")),
+      BashScript(path = Some("bar.sh")),
+      BashScript(path = Some("baz.sh")),
+    )
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isDefined)
+    assert(mainScript.get.path == Some("foo.sh"))
+    assert(additionalResources.length == 2)
+  }
+
+  test("Single text file") {
+    val resources = List(PlainFile(path = Some("foo.txt")))
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isEmpty)
+    assert(additionalResources.length == 1)
+    assert(additionalResources.head.path == Some("foo.txt"))
+  }
+
+  test("Multiple text files") {
+    val resources = List(
+      PlainFile(path = Some("foo.txt")),
+      PlainFile(path = Some("bar.txt")),
+      PlainFile(path = Some("baz.txt")),
+    )
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isEmpty)
+    assert(additionalResources.length == 3)
+  }
+
+  test("Mixed Script and text files, first is script") {
+    val resources = List(
+      BashScript(path = Some("foo.sh")),
+      PlainFile(path = Some("bar.txt")),
+      BashScript(path = Some("baz.sh")),
+    )
+
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isDefined)
+    assert(mainScript.get.path == Some("foo.sh"))
+    assert(additionalResources.length == 2)
+  }
+
+  test("Mixed Script and text files, first is text file") {
+    val resources = List(
+      PlainFile(path = Some("foo.txt")),
+      BashScript(path = Some("bar.sh")),
+      PlainFile(path = Some("baz.txt")),
+    )
+
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isEmpty)
+    assert(additionalResources.length == 3)
+  }
+
+  test("No resources") {
+    val resources = List.empty
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isEmpty)
+    assert(additionalResources.isEmpty)
+  }
+}
\ No newline at end of file
diff --git a/src/test/scala/io/viash/helpers/IOTest.scala b/src/test/scala/io/viash/helpers/IOTest.scala
index 97bde729c..0159d3007 100644
--- a/src/test/scala/io/viash/helpers/IOTest.scala
+++ b/src/test/scala/io/viash/helpers/IOTest.scala
@@ -22,11 +22,62 @@ class IOTest extends AnyFunSuite with BeforeAndAfter {
   test("makeTemp and deleteRecursively") {
     val temp = IO.makeTemp("foo")
     assert(Files.exists(temp) && Files.isDirectory(temp))
+    assert(temp.toString.matches(".*foo[\\w]+"), "Temporary directory name should be randomized, strategy can differ between platforms.")
 
     IO.deleteRecursively(temp)
     assert(!Files.exists(temp))
   }
 
+  test("makeTemp with addRandomized disabled, folder exists") {
+    val tempDir = IO.makeTemp("foo")
+    val tempDirStr = tempDir.getFileName().toString()
+    val newTemp = IO.makeTemp(tempDirStr, addRandomized = false)
+    assert(Files.exists(newTemp) && Files.isDirectory(newTemp))
+
+    assert(newTemp == tempDir)
+    IO.deleteRecursively(newTemp)
+  }
+
+  test("makeTemp with addRandomized disabled, folder doesn't exist") {
+    val tempDir = IO.makeTemp("foo")
+    val tempDirStr = tempDir.getFileName().toString()
+    IO.deleteRecursively(tempDir)
+    val newTemp = IO.makeTemp(tempDirStr, addRandomized = false)
+    assert(Files.exists(newTemp) && Files.isDirectory(newTemp))
+
+    assert(newTemp == tempDir)
+    IO.deleteRecursively(newTemp)
+  }
+
+  test("makeTemp with addRandomized disabled, folder exists but not empty") {
+    val tempDir = IO.makeTemp("foo")
+    val tempDirStr = tempDir.getFileName().toString()
+    IO.write("foo", tempDir.resolve("foo.txt"))
+
+    val caught = intercept[RuntimeException] {
+      IO.makeTemp(tempDirStr, addRandomized = false)
+    }
+
+    assert(caught.getMessage().contains(s"Temporary directory $tempDir already exists and is not empty."))
+
+    IO.deleteRecursively(tempDir)
+  }
+
+  test("makeTemp with addRandomized disabled, folder exists as a file") {
+    val tempDir = IO.makeTemp("foo")
+    val tempDirStr = tempDir.getFileName().toString()
+    IO.deleteRecursively(tempDir)
+    IO.write("foo", tempDir)
+
+    val caught = intercept[RuntimeException] {
+      IO.makeTemp(tempDirStr, addRandomized = false)
+    }
+
+    assert(caught.getMessage().contains(s"Temporary directory $tempDir already exists as a file."))
+
+    IO.deleteRecursively(tempDir)
+  }
+
   test("uri with path") {
     val uri = IO.uri("test.txt")
     assert(uri.isInstanceOf[URI])
diff --git a/src/test/scala/io/viash/platforms/nextflow/NextflowScriptTest.scala b/src/test/scala/io/viash/platforms/nextflow/NextflowScriptTest.scala
index 02673886c..cf0b689da 100644
--- a/src/test/scala/io/viash/platforms/nextflow/NextflowScriptTest.scala
+++ b/src/test/scala/io/viash/platforms/nextflow/NextflowScriptTest.scala
@@ -14,6 +14,14 @@ import java.io.UncheckedIOException
 
 import NextflowTestHelper._
 
+/**
+  * This test suite contains tests related to the NextflowScript class.
+  * 
+  * All workflows tested in this suite should be self-contained in that
+  * they execute tests and do assertions within the same workflow. If
+  * the test fails, the workflow should print a helpful error message and
+  * exit with a non-zero exit code.
+  */
 class NextflowScriptTest extends AnyFunSuite with BeforeAndAfterAll {
   Logger.UseColorOverride.value = Some(false)
   // temporary folder to work in
@@ -145,8 +153,15 @@ class NextflowScriptTest extends AnyFunSuite with BeforeAndAfterAll {
     )
 
     assert(exitCode == 0, s"\nexit code was $exitCode\nStd output:\n$stdOut\nStd error:\n$stdErr")
-    assert(stdOut.contains("base:step1_alias:proc"))
-    assert(stdOut.contains("base:step1:proc"))
+    // Note: Nextflow 23.04 changed the way processes are printed in the log
+    // original:
+    //   [info]   [30/b6eaaf] process > alias:base:step1:processWf:... [100%] 1 of 1 ✔
+    //   [info]   [bf/166913] process > alias:base:step1_alias:proc... [100%] 1 of 1 ✔
+    // since nextflow 23.04:
+    //   [info]   [31/1c0834] ali…cessWf:step1_process (one) | 1 of 1 ✔
+    //   [info]   [f1/e92549] ali…:step1_alias_process (one) | 1 of 1 ✔
+    assert(stdOut.contains(":step1_alias:proc") || stdOut.contains(":step1_alias_process"))
+    assert(stdOut.contains(":step1:proc") || stdOut.contains(":step1_process"))
     assert(!stdOut.contains("Key for module 'step1' is duplicated"))
   }
 
@@ -202,7 +217,6 @@ class NextflowScriptTest extends AnyFunSuite with BeforeAndAfterAll {
     assert(exitCode == 0, s"\nexit code was $exitCode\nStd output:\n$stdOut1\nStd error:\n$stdErr1")
   }
 
-
   override def afterAll(): Unit = {
     IO.deleteRecursively(temporaryFolder)
   }
diff --git a/src/test/scala/io/viash/platforms/nextflow/Vdsl3StandaloneTest.scala b/src/test/scala/io/viash/platforms/nextflow/Vdsl3StandaloneTest.scala
index 6ba262c72..c664f0b0e 100644
--- a/src/test/scala/io/viash/platforms/nextflow/Vdsl3StandaloneTest.scala
+++ b/src/test/scala/io/viash/platforms/nextflow/Vdsl3StandaloneTest.scala
@@ -8,6 +8,7 @@ import java.io.UncheckedIOException
 import java.io.File
 import java.nio.file.{Files, Path, Paths}
 import scala.io.Source
+import scala.util.Using
 
 import io.viash.helpers.{IO, Logger}
 import io.viash.{DockerTest, NextflowTest, TestHelper}
@@ -15,6 +16,11 @@ import java.nio.charset.StandardCharsets
 
 import NextflowTestHelper._
 
+/**
+  * Test suite for VDSL3 components as standalone Nextflow workflows.
+  * Since these tests run workflows from the CLI, we need to check the
+  * generated output inside the test suite.
+  */
 class Vdsl3StandaloneTest extends AnyFunSuite with BeforeAndAfterAll {
   Logger.UseColorOverride.value = Some(false)
   // temporary folder to work in
@@ -163,6 +169,48 @@ class Vdsl3StandaloneTest extends AnyFunSuite with BeforeAndAfterAll {
     }
   }
 
+
+  test("Run multiple output test", NextflowTest) {
+    val (exitCode, stdOut, stdErr) = NextflowTestHelper.run(
+      mainScript = "target/nextflow/multiple_output/main.nf",
+      args = List(
+        "--id", "foo",
+        "--input", "resources/lines*.txt",
+        "--publish_dir", "multipleOutput"
+      ),
+      cwd = tempFolFile
+    )
+
+    assert(exitCode == 0, s"\nexit code was $exitCode\nStd output:\n$stdOut\nStd error:\n$stdErr")
+
+    val expectedFiles =
+      Map(
+        "state" -> "state.yaml",
+        "output_0" -> "output_0.txt", 
+        "output_1" -> "output_1.txt"
+      ).map{ case (id, suffix) =>
+        val path = temporaryFolder.resolve("multipleOutput/foo.multiple_output." + suffix)
+        (id, path)
+      }
+
+    // check if files exist
+    for ((id, path) <- expectedFiles) {
+      assert(Files.exists(path), s"File '$id' at path '$path' does not exist")
+    }
+
+    // check state content
+    Using(Source.fromFile(expectedFiles("state").toFile())) { reader =>
+      val stateTxt = reader.getLines().mkString("\n")
+      val expectedState = """\
+        |id: foo
+        |output:
+        |- !file 'foo.multiple_output.output_0.txt'
+        |- !file 'foo.multiple_output.output_1.txt'
+        |""".stripMargin
+      assert(stateTxt == expectedState)
+    }
+  }
+
   override def afterAll(): Unit = {
     IO.deleteRecursively(temporaryFolder)
   }