Build branch main with version main (f52978a)

Build pipeline: viash-hub.rnaseq.main-k4ttq

Source commit: f52978a0e2

Source message: Fix summarizedexperiment build (#42)

CHANGELOG.md

@@ -1,9 +1,10 @@
-# RNAseq version x.y.z
+# rnaseq v0.2.1
 
-## Changes
+## Bug fixes
 
-- Add resources labels
-- Increase the number of components that are fetched from BioBox
+* Fix `summarizedexperiment` build PR (#42).
+ 
+* Fix an issue with the `deseq2_qc` component not being able to create the DESeq2 object (PR #41).
 
 ## Known issues
 

_viash.yaml

@@ -1,13 +1,13 @@
 name: rnaseq
 
-viash_version: 0.9.0
+viash_version: 0.9.2
 
 source: src
 target: target
 
 info:
   test_resources:
-    - path: gs://viash-hub-test-data/rnaseq/v1
+    - path: gs://viash-hub-resources/rnaseq/v1
       dest: testData
 
 config_mods: |

src/assets/optional_file.txt

@@ -0,0 +1 @@
+Optional!

src/assets/required_file.txt

@@ -0,0 +1 @@
+Required!

src/deseq2_qc/config.vsh.yaml

@@ -68,8 +68,16 @@ test_resources:
 
 engines: 
   - type: docker
-    image: rocker/r2u:22.04
+    image: debian:latest
     setup:
+      - type: apt
+        packages:
+          - libcurl4-openssl-dev
+          - r-base
+          - r-base-core
+          - libxml2-dev
+          - procps
+          - libssl-dev
       - type: r
         cran: [ optparse, ggplot2, RColorBrewer, pheatmap, stringr, matrixStats ]
         bioc: [ DESeq2 ]

src/deseq2_qc/script.r

@@ -8,7 +8,8 @@ par <- list(
   deseq2_output = "deseq2",
   pca_multiqc = "pca.vals_mqc.tsv",
   dists_multiqc = "sample.dists_mqc.tsv",
-  vst = FALSE
+  vst = FALSE,
+  outdir = '.'
 )
 meta <- list(
   resources_dir = "src/deseq2_qc"
@@ -100,7 +101,7 @@ saveRDS(dds, file = sub("\\.dds\\.RData$", ".rds", DDSFile))
 ##' @author Gavin Kelly
 
 plotPCA_vst <- function(object,  ntop = 500, assay = length(assays(object))) {
-  rv <- rowVars(assay(object, assay))
+  rv <- rowVars(assay(object, assay), useNames = TRUE)
   select <- order(rv, decreasing = TRUE)[seq_len(min(ntop, length(rv)))]
   pca <- prcomp(t(assay(object, assay)[select, ]), center = TRUE, scale = FALSE)
   percentVar <- pca$sdev^2 / sum(pca$sdev^2)

src/extra/copy_if_exists/config.vsh.yaml

@@ -0,0 +1,32 @@
+name: "copy_if_exists"
+argument_groups: 
+  - name: "Input"
+    arguments:
+      - name: "--required_file"
+        type: file
+        must_exist: false
+        required: true
+        example: /tmp/rnaseq_workflow_config/required_file.txt
+      - name: --optional_file
+        type: file
+        must_exist: false
+        example: /tmp/rnaseq_workflow_config/optional_file.txt
+
+  - name: "Ouput"
+    arguments:
+      - name: "--output"
+        type: file
+        direction: output
+        default: copy_if_exists_output
+resources:
+  - type: bash_script
+    path: script.sh
+  - path: /src/assets/required_file.txt
+  - path: /src/assets/optional_file.txt
+
+engines:
+  - type: docker
+    image: ubuntu:22.04
+runners:
+  - type: executable
+  - type: nextflow

src/extra/copy_if_exists/script.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+set -eo pipefail
+
+mkdir -p $par_output
+
+# This file is checked by the Nextflow module wrapper
+cp $par_required_file "$par_output"
+
+# If the variable is empty, we use the default one (registered as a resource)
+if [ -z $par_optional_file ]; then
+  echo "No optional_file provided, using the default"
+  cp $meta_resources_dir/optional_file.txt "$par_output"
+else
+  echo "Optional file provided"
+  if [ -f $par_optional_file ]; then
+    cp $par_optional_file "$par_output"
+  else
+    # Unreachable: the Viash-generated module checks this
+    echo "Optional file does not exist"
+    exit 1
+  fi
+fi
+
+echo "Done"

src/summarizedexperiment/config.vsh.yaml

@@ -39,10 +39,8 @@ resources:
   
 engines:
 - type: docker
-  image: ubuntu:22.04
+  image: rocker/r2u:22.04
   setup:
-    - type: apt
-      packages: [ r-base, libcurl4-openssl-dev ]
     - type: r
       bioc: [ SummarizedExperiment, tximeta ]
 runners: 

target/dependencies/vsh/vsh/biobox/main/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml

@@ -267,6 +267,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -367,16 +370,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bbmap/bbmap_bbsplit"
   executable: "target/nextflow/bbmap/bbmap_bbsplit/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/bbmap/bbmap_bbsplit/main.nf

@@ -1,6 +1,6 @@
 // bbmap_bbsplit main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -173,7 +168,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +187,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +201,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1664,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1877,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1889,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1901,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1942,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1962,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1993,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2003,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2687,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2845,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2887,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2983,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3101,6 +3327,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3219,16 +3449,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bbmap/bbmap_bbsplit",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3729,7 +3959,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3743,6 +3973,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json

@@ -187,10 +187,10 @@
                 "index": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.index.index`, example: `BBSplit_index`. Location to write the index",
-                "help_text": "Type: `file`, default: `$id.$key.index.index`, example: `BBSplit_index`. Location to write the index.\n"
+                "description": "Type: `file`, default: `$id.$key.index`, example: `BBSplit_index`. Location to write the index",
+                "help_text": "Type: `file`, default: `$id.$key.index`, example: `BBSplit_index`. Location to write the index.\n"
             ,
-                "default":"$id.$key.index.index"
+                "default":"$id.$key.index"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml

@@ -226,6 +226,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -336,16 +339,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bedtools/bedtools_genomecov"
   executable: "target/nextflow/bedtools/bedtools_genomecov/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/bedtools/bedtools_genomecov/main.nf

@@ -1,6 +1,6 @@
 // bedtools_genomecov main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3073,6 +3299,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3206,16 +3436,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_genomecov",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3677,7 +3907,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3691,6 +3921,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml

@@ -982,6 +982,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -1082,16 +1085,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/fastp"
   executable: "target/nextflow/fastp/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf

@@ -1,6 +1,6 @@
 // fastp main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3901,6 +4127,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -4022,16 +4252,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/fastp",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -4606,7 +4836,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -4620,6 +4850,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/nextflow_schema.json

@@ -102,10 +102,10 @@
                 "overlapped_out": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.overlapped_out.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base",
-                "help_text": "Type: `file`, default: `$id.$key.overlapped_out.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base.\n"
+                "description": "Type: `file`, default: `$id.$key.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base",
+                "help_text": "Type: `file`, default: `$id.$key.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base.\n"
             ,
-                "default":"$id.$key.overlapped_out.overlapped_out"
+                "default":"$id.$key.overlapped_out"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/fastqc/.config.vsh.yaml

@@ -239,6 +239,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -339,16 +342,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/fastqc"
   executable: "target/nextflow/fastqc/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/fastqc/main.nf

@@ -1,6 +1,6 @@
 // fastqc main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3062,6 +3288,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3181,16 +3411,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/fastqc",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3678,7 +3908,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3692,6 +3922,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml

@@ -543,6 +543,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -644,16 +647,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/featurecounts"
   executable: "target/nextflow/featurecounts/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf

@@ -1,6 +1,6 @@
 // featurecounts main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3427,6 +3653,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3548,16 +3778,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/featurecounts",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3662,7 +3892,7 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
 ## VIASH END
 
 # create temporary directory
-tmp_dir=\\$(mktemp -d -p "\\$meta_temp_dir" "\\${meta_functionality_name}_XXXXXX")
+tmp_dir=\\$(mktemp -d -p "\\$meta_temp_dir" "\\${meta_name}_XXXXXX")
 mkdir -p "\\$tmp_dir/temp"
 
 # create detailed_results directory if variable is set and directory does not exist
@@ -4089,7 +4319,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -4103,6 +4333,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/nextflow_schema.json

@@ -573,10 +573,10 @@
                 "detailed_results": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.detailed_results.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results",
-                "help_text": "Type: `file`, default: `$id.$key.detailed_results.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results. Use `--detailed_results_format` to determine the format of the detailed results.\n"
+                "description": "Type: `file`, default: `$id.$key.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results",
+                "help_text": "Type: `file`, default: `$id.$key.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results. Use `--detailed_results_format` to determine the format of the detailed results.\n"
             ,
-                "default":"$id.$key.detailed_results.detailed_results"
+                "default":"$id.$key.detailed_results"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/fq_subsample/.config.vsh.yaml

@@ -88,6 +88,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -189,16 +192,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/fq_subsample"
   executable: "target/nextflow/fq_subsample/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/fq_subsample/main.nf

@@ -1,6 +1,6 @@
 // fq_subsample main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -173,7 +168,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +187,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +201,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1664,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1877,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1889,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1901,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1942,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1962,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1993,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2003,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2687,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2845,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2887,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2983,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2914,6 +3140,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3031,16 +3261,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/fq_subsample",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3459,7 +3689,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3473,6 +3703,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/fq_subsample/nextflow_schema.json

@@ -47,10 +47,10 @@
                 "output_1": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output_1.output_1`. Sampled read 1 fastq files",
-                "help_text": "Type: `file`, default: `$id.$key.output_1.output_1`. Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`."
+                "description": "Type: `file`, default: `$id.$key.output_1`. Sampled read 1 fastq files",
+                "help_text": "Type: `file`, default: `$id.$key.output_1`. Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`."
             ,
-                "default":"$id.$key.output_1.output_1"
+                "default":"$id.$key.output_1"
             }
     
 
@@ -58,10 +58,10 @@
                 "output_2": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output_2.output_2`. Sampled read 2 fastq files",
-                "help_text": "Type: `file`, default: `$id.$key.output_2.output_2`. Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`."
+                "description": "Type: `file`, default: `$id.$key.output_2`. Sampled read 2 fastq files",
+                "help_text": "Type: `file`, default: `$id.$key.output_2`. Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`."
             ,
-                "default":"$id.$key.output_2.output_2"
+                "default":"$id.$key.output_2"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml

@@ -582,6 +582,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -684,16 +687,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/gffread"
   executable: "target/nextflow/gffread/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf

@@ -1,6 +1,6 @@
 // gffread main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3482,6 +3708,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3605,16 +3835,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/gffread",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -4192,7 +4422,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -4206,6 +4436,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_index/.config.vsh.yaml

@@ -113,6 +113,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -217,16 +220,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/kallisto/kallisto_index"
   executable: "target/nextflow/kallisto/kallisto_index/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_index/main.nf

@@ -1,6 +1,6 @@
 // kallisto_index main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -173,7 +168,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +187,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +201,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1664,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1877,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1889,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1901,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1942,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1962,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1993,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2003,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2687,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2845,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2887,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2983,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2948,6 +3174,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3070,16 +3300,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/kallisto/kallisto_index",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3509,7 +3739,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3523,6 +3753,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_index/nextflow_schema.json

@@ -47,10 +47,10 @@
                 "index": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.index.index`, example: `Kallisto_index`. ",
-                "help_text": "Type: `file`, default: `$id.$key.index.index`, example: `Kallisto_index`. "
+                "description": "Type: `file`, default: `$id.$key.index`, example: `Kallisto_index`. ",
+                "help_text": "Type: `file`, default: `$id.$key.index`, example: `Kallisto_index`. "
             ,
-                "default":"$id.$key.index.index"
+                "default":"$id.$key.index"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_quant/.config.vsh.yaml

@@ -137,6 +137,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -245,16 +248,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/kallisto/kallisto_quant"
   executable: "target/nextflow/kallisto/kallisto_quant/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_quant/main.nf

@@ -1,6 +1,6 @@
 // kallisto_quant main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -173,7 +168,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +187,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +201,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1664,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1877,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1889,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1901,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1942,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1962,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1993,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2003,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2687,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2845,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2887,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2983,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2975,6 +3201,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3104,16 +3334,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/kallisto/kallisto_quant",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3557,7 +3787,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3571,6 +3801,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_quant/nextflow_schema.json

@@ -47,10 +47,10 @@
                 "output_dir": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. Directory to write output to",
-                "help_text": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. Directory to write output to."
+                "description": "Type: `file`, required, default: `$id.$key.output_dir`. Directory to write output to",
+                "help_text": "Type: `file`, required, default: `$id.$key.output_dir`. Directory to write output to."
             ,
-                "default":"$id.$key.output_dir.output_dir"
+                "default":"$id.$key.output_dir"
             }
     
 
@@ -58,10 +58,10 @@
                 "log": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.log.log`. File containing log information from running kallisto quant",
-                "help_text": "Type: `file`, default: `$id.$key.log.log`. File containing log information from running kallisto quant"
+                "description": "Type: `file`, default: `$id.$key.log`. File containing log information from running kallisto quant",
+                "help_text": "Type: `file`, default: `$id.$key.log`. File containing log information from running kallisto quant"
             ,
-                "default":"$id.$key.log.log"
+                "default":"$id.$key.log"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml

@@ -357,6 +357,9 @@ info:
     doi: "10.1093/bioinformatics/btw354"
   licence: "GPL v3 or later"
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -455,16 +458,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/multiqc"
   executable: "target/nextflow/multiqc/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf

@@ -1,6 +1,6 @@
 // multiqc main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3246,6 +3472,10 @@ meta = [
     "licence" : "GPL v3 or later"
   },
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3365,16 +3595,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/multiqc",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3935,7 +4165,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3949,6 +4179,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/nextflow_schema.json

@@ -48,10 +48,10 @@
                 "output_data": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files",
-                "help_text": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files. If not provided, parsed data will not be published.\n"
+                "description": "Type: `file`, default: `$id.$key.output_data`, example: `multiqc_data`. Output directory for parsed data files",
+                "help_text": "Type: `file`, default: `$id.$key.output_data`, example: `multiqc_data`. Output directory for parsed data files. If not provided, parsed data will not be published.\n"
             ,
-                "default":"$id.$key.output_data.output_data"
+                "default":"$id.$key.output_data"
             }
     
 
@@ -59,10 +59,10 @@
                 "output_plots": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots",
-                "help_text": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots. If not provided, plots will not be published.\n"
+                "description": "Type: `file`, default: `$id.$key.output_plots`, example: `multiqc_plots`. Output directory for generated plots",
+                "help_text": "Type: `file`, default: `$id.$key.output_plots`, example: `multiqc_plots`. Output directory for generated plots. If not provided, plots will not be published.\n"
             ,
-                "default":"$id.$key.output_plots.output_plots"
+                "default":"$id.$key.output_plots"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml

@@ -161,6 +161,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -263,16 +266,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/qualimap/qualimap_rnaseq"
   executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/qualimap/qualimap_rnaseq/main.nf

@@ -1,6 +1,6 @@
 // qualimap_rnaseq main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3005,6 +3231,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3128,16 +3358,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/qualimap/qualimap_rnaseq",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3588,7 +3818,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3602,6 +3832,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json

@@ -58,10 +58,10 @@
                 "counts": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.counts.counts`. Output file for computed counts",
-                "help_text": "Type: `file`, default: `$id.$key.counts.counts`. Output file for computed counts."
+                "description": "Type: `file`, default: `$id.$key.counts`. Output file for computed counts",
+                "help_text": "Type: `file`, default: `$id.$key.counts`. Output file for computed counts."
             ,
-                "default":"$id.$key.counts.counts"
+                "default":"$id.$key.counts"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml

@@ -724,6 +724,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -851,16 +854,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/rsem/rsem_calculate_expression"
   executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_calculate_expression/main.nf

@@ -1,6 +1,6 @@
 // rsem_calculate_expression main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -173,7 +168,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +187,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +201,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1664,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1877,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1889,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1901,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1942,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1962,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1993,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2003,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2687,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2845,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2887,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2983,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3514,6 +3740,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3660,16 +3890,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/rsem/rsem_calculate_expression",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -4221,7 +4451,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -4235,6 +4465,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml

@@ -268,6 +268,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -415,16 +418,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/rsem/rsem_prepare_reference"
   executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf

@@ -1,6 +1,6 @@
 // rsem_prepare_reference main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3085,6 +3311,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3244,16 +3474,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/rsem/rsem_prepare_reference",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3705,7 +3935,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3719,6 +3949,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json

@@ -47,10 +47,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.output.output`. Directory containing reference files generated by RSEM",
-                "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Directory containing reference files generated by RSEM."
+                "description": "Type: `file`, required, default: `$id.$key.output`. Directory containing reference files generated by RSEM",
+                "help_text": "Type: `file`, required, default: `$id.$key.output`. Directory containing reference files generated by RSEM."
             ,
-                "default":"$id.$key.output.output"
+                "default":"$id.$key.output"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml

@@ -68,6 +68,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -174,16 +177,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/rseqc/rseqc_bamstat"
   executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat/main.nf

@@ -1,6 +1,6 @@
 // rseqc_bamstat main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2905,6 +3131,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3035,16 +3265,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/rseqc/rseqc_bamstat",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3445,7 +3675,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3459,6 +3689,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json

@@ -47,10 +47,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output.output`. Output file (txt) with mapping quality statistics",
-                "help_text": "Type: `file`, default: `$id.$key.output.output`. Output file (txt) with mapping quality statistics."
+                "description": "Type: `file`, default: `$id.$key.output`. Output file (txt) with mapping quality statistics",
+                "help_text": "Type: `file`, default: `$id.$key.output`. Output file (txt) with mapping quality statistics."
             ,
-                "default":"$id.$key.output.output"
+                "default":"$id.$key.output"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml

@@ -96,6 +96,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -200,16 +203,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/rseqc/rseqc_inferexperiment"
   executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inferexperiment/main.nf

@@ -1,6 +1,6 @@
 // rseqc_inferexperiment main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2942,6 +3168,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3068,16 +3298,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/rseqc/rseqc_inferexperiment",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3481,7 +3711,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3495,6 +3725,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml

@@ -185,6 +185,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -293,16 +296,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/rseqc/rseqc_inner_distance"
   executable: "target/nextflow/rseqc/rseqc_inner_distance/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inner_distance/main.nf

@@ -1,6 +1,6 @@
 // rseqc_inner_distance main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3035,6 +3261,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3168,16 +3398,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/rseqc/rseqc_inner_distance",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3604,7 +3834,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3618,6 +3848,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json

@@ -107,10 +107,10 @@
                 "output_stats": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output_stats.output_stats`. output file (txt) with summary statistics of inner distances of paired reads",
-                "help_text": "Type: `file`, default: `$id.$key.output_stats.output_stats`. output file (txt) with summary statistics of inner distances of paired reads"
+                "description": "Type: `file`, default: `$id.$key.output_stats`. output file (txt) with summary statistics of inner distances of paired reads",
+                "help_text": "Type: `file`, default: `$id.$key.output_stats`. output file (txt) with summary statistics of inner distances of paired reads"
             ,
-                "default":"$id.$key.output_stats.output_stats"
+                "default":"$id.$key.output_stats"
             }
     
 
@@ -118,10 +118,10 @@
                 "output_dist": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output_dist.output_dist`. output file (txt) with inner distances of all paired reads",
-                "help_text": "Type: `file`, default: `$id.$key.output_dist.output_dist`. output file (txt) with inner distances of all paired reads"
+                "description": "Type: `file`, default: `$id.$key.output_dist`. output file (txt) with inner distances of all paired reads",
+                "help_text": "Type: `file`, default: `$id.$key.output_dist`. output file (txt) with inner distances of all paired reads"
             ,
-                "default":"$id.$key.output_dist.output_dist"
+                "default":"$id.$key.output_dist"
             }
     
 
@@ -129,10 +129,10 @@
                 "output_freq": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output_freq.output_freq`. output file (txt) with frequencies of inner distances of all paired reads",
-                "help_text": "Type: `file`, default: `$id.$key.output_freq.output_freq`. output file (txt) with frequencies of inner distances of all paired reads"
+                "description": "Type: `file`, default: `$id.$key.output_freq`. output file (txt) with frequencies of inner distances of all paired reads",
+                "help_text": "Type: `file`, default: `$id.$key.output_freq`. output file (txt) with frequencies of inner distances of all paired reads"
             ,
-                "default":"$id.$key.output_freq.output_freq"
+                "default":"$id.$key.output_freq"
             }
     
 
@@ -140,10 +140,10 @@
                 "output_plot": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output_plot.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads",
-                "help_text": "Type: `file`, default: `$id.$key.output_plot.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads"
+                "description": "Type: `file`, default: `$id.$key.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads",
+                "help_text": "Type: `file`, default: `$id.$key.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads"
             ,
-                "default":"$id.$key.output_plot.output_plot"
+                "default":"$id.$key.output_plot"
             }
     
 
@@ -151,10 +151,10 @@
                 "output_plot_r": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output_plot_r.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads",
-                "help_text": "Type: `file`, default: `$id.$key.output_plot_r.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads"
+                "description": "Type: `file`, default: `$id.$key.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads",
+                "help_text": "Type: `file`, default: `$id.$key.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads"
             ,
-                "default":"$id.$key.output_plot_r.output_plot_r"
+                "default":"$id.$key.output_plot_r"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml

@@ -176,6 +176,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -276,16 +279,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/salmon/salmon_index"
   executable: "target/nextflow/salmon/salmon_index/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf

@@ -1,6 +1,6 @@
 // salmon_index main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3007,6 +3233,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3128,16 +3358,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/salmon/salmon_index",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3224,7 +3454,7 @@ for par in \\${unset_if_false[@]}; do
     [[ "\\$test_val" == "false" ]] && unset \\$par
 done
 
-tmp_dir=\\$(mktemp -d -p "\\$meta_temp_dir" "\\${meta_functionality_name}_XXXXXX")
+tmp_dir=\\$(mktemp -d -p "\\$meta_temp_dir" "\\${meta_name}_XXXXXX")
 mkdir -p "\\$tmp_dir/temp"
 
 if [[ -f "\\$par_genome" ]] && [[ ! "\\$par_decoys" ]]; then
@@ -3593,7 +3823,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3607,6 +3837,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/nextflow_schema.json

@@ -153,10 +153,10 @@
                 "index": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.index.index`, example: `Salmon_index`. Salmon index\n",
-                "help_text": "Type: `file`, required, default: `$id.$key.index.index`, example: `Salmon_index`. Salmon index\n"
+                "description": "Type: `file`, required, default: `$id.$key.index`, example: `Salmon_index`. Salmon index\n",
+                "help_text": "Type: `file`, required, default: `$id.$key.index`, example: `Salmon_index`. Salmon index\n"
             ,
-                "default":"$id.$key.index.index"
+                "default":"$id.$key.index"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml

@@ -1072,6 +1072,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -1172,16 +1175,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/salmon/salmon_quant"
   executable: "target/nextflow/salmon/salmon_quant/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf

@@ -1,6 +1,6 @@
 // salmon_quant main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3842,6 +4068,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3963,16 +4193,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/salmon/salmon_quant",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -4608,7 +4838,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -4622,6 +4852,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/nextflow_schema.json

@@ -152,10 +152,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.output.output`, example: `quant_output`. Output quantification directory",
-                "help_text": "Type: `file`, required, default: `$id.$key.output.output`, example: `quant_output`. Output quantification directory.\n"
+                "description": "Type: `file`, required, default: `$id.$key.output`, example: `quant_output`. Output quantification directory",
+                "help_text": "Type: `file`, required, default: `$id.$key.output`, example: `quant_output`. Output quantification directory.\n"
             ,
-                "default":"$id.$key.output.output"
+                "default":"$id.$key.output"
             }
     
 
@@ -584,10 +584,10 @@
                 "aux_dir": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.aux_dir.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e",
-                "help_text": "Type: `file`, default: `$id.$key.aux_dir.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e.g. bootstraps, bias parameters, etc. will be written.\n"
+                "description": "Type: `file`, default: `$id.$key.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e",
+                "help_text": "Type: `file`, default: `$id.$key.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e.g. bootstraps, bias parameters, etc. will be written.\n"
             ,
-                "default":"$id.$key.aux_dir.aux_dir"
+                "default":"$id.$key.aux_dir"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml

@@ -66,6 +66,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -172,16 +175,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_flagstat"
   executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf

@@ -1,6 +1,6 @@
 // samtools_flagstat main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2901,6 +3127,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3027,16 +3257,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_flagstat",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3437,7 +3667,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3451,6 +3681,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml

@@ -75,6 +75,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -182,16 +185,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_idxstats"
   executable: "target/nextflow/samtools/samtools_idxstats/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf

@@ -1,6 +1,6 @@
 // samtools_idxstats main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2912,6 +3138,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3039,16 +3269,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_idxstats",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3447,7 +3677,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3461,6 +3691,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml

@@ -84,6 +84,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -188,16 +191,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_index"
   executable: "target/nextflow/samtools/samtools_index/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf

@@ -1,6 +1,6 @@
 // samtools_index main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2928,6 +3154,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3052,16 +3282,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_index",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3471,7 +3701,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3485,6 +3715,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml

@@ -227,6 +227,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -331,16 +334,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_sort"
   executable: "target/nextflow/samtools/samtools_sort/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf

@@ -1,6 +1,6 @@
 // samtools_sort main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3100,6 +3326,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3224,16 +3454,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_sort",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3691,7 +3921,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3705,6 +3935,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml

@@ -295,6 +295,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -400,16 +403,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_stats"
   executable: "target/nextflow/samtools/samtools_stats/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf

@@ -1,6 +1,6 @@
 // samtools_stats main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3169,6 +3395,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3294,16 +3524,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_stats",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3753,7 +3983,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3767,6 +3997,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/sortmerna/.config.vsh.yaml

@@ -487,6 +487,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -593,16 +596,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/sortmerna"
   executable: "target/nextflow/sortmerna/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/sortmerna/main.nf

@@ -1,6 +1,6 @@
 // sortmerna main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -173,7 +168,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +187,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +201,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1664,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1877,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1889,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1901,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1942,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1962,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1993,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2003,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2687,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2845,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2887,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2983,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3333,6 +3559,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3459,16 +3689,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/sortmerna",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -4003,7 +4233,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -4017,6 +4247,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/sortmerna/nextflow_schema.json

@@ -79,10 +79,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output.output`. Directory and file prefix for aligned output",
-                "help_text": "Type: `file`, default: `$id.$key.output.output`. Directory and file prefix for aligned output. The appropriate extension: \n(fasta|fastq|blast|sam|etc) is automatically added.\nIf \u0027dir\u0027 is not specified, the output is created in the WORKDIR/out/.\nIf \u0027pfx\u0027 is not specified, the prefix \u0027aligned\u0027 is used.\n"
+                "description": "Type: `file`, default: `$id.$key.output`. Directory and file prefix for aligned output",
+                "help_text": "Type: `file`, default: `$id.$key.output`. Directory and file prefix for aligned output. The appropriate extension: \n(fasta|fastq|blast|sam|etc) is automatically added.\nIf \u0027dir\u0027 is not specified, the output is created in the WORKDIR/out/.\nIf \u0027pfx\u0027 is not specified, the prefix \u0027aligned\u0027 is used.\n"
             ,
-                "default":"$id.$key.output.output"
+                "default":"$id.$key.output"
             }
     
 
@@ -90,10 +90,10 @@
                 "other": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.other.other`. Create Non-aligned reads output file with this path/prefix",
-                "help_text": "Type: `file`, default: `$id.$key.other.other`. Create Non-aligned reads output file with this path/prefix. Must be used with fastx."
+                "description": "Type: `file`, default: `$id.$key.other`. Create Non-aligned reads output file with this path/prefix",
+                "help_text": "Type: `file`, default: `$id.$key.other`. Create Non-aligned reads output file with this path/prefix. Must be used with fastx."
             ,
-                "default":"$id.$key.other.other"
+                "default":"$id.$key.other"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml

@@ -2540,6 +2540,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -2662,16 +2665,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/star/star_align_reads"
   executable: "target/nextflow/star/star_align_reads/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf

@@ -1,6 +1,6 @@
 // star_align_reads main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -177,7 +172,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -196,15 +191,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -217,6 +205,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1670,6 +1668,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1727,8 +1881,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1741,7 +1893,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1753,33 +1905,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1810,13 +1946,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1833,7 +1966,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1864,13 +1997,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1878,18 +2007,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2563,7 +2691,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2720,12 +2849,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2738,19 +2891,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2759,23 +2987,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -5794,6 +6020,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -5942,16 +6172,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/star/star_align_reads",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -5982,7 +6212,7 @@ meta = [
 // inner workflow hook
 def innerWorkflowFactory(args) {
   def rawScript = '''set -e
-tempscript=".viash_script.sh"
+tempscript=".viash_script.py"
 cat > "$tempscript" << VIASHMAIN
 import tempfile
 import subprocess
@@ -6645,7 +6875,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -6659,6 +6889,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml

@@ -221,6 +221,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -332,16 +335,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/star/star_genome_generate"
   executable: "target/nextflow/star/star_genome_generate/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf

@@ -1,6 +1,6 @@
 // star_genome_generate main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3063,6 +3289,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3194,16 +3424,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/star/star_genome_generate",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3292,10 +3522,10 @@ STAR \\\\
     \\${par_genome_sa_index_nbases:+--genomeSAindexNbases "\\${par_genome_sa_index_nbases}"} \\\\
     \\${par_sjdb_gtf_chr_prefix:+--sjdbGTFchrPrefix "\\${par_sjdb_gtf_chr_prefix}"} \\\\
     \\${par_sjdb_gtf_feature_exon:+--sjdbGTFfeatureExon "\\${par_sjdb_gtf_feature_exon}"} \\\\
-    \\${par_sjdb_gtf_tag_exon_parent_transcript:+--sjdbGTFtag_exon_parent_transcript "\\${par_sjdb_gtf_tag_exon_parent_transcript}"} \\\\
-    \\${par_sjdb_gtf_tag_exon_parent_gene:+--sjdbGTFtag_exon_parent_gene "\\${par_sjdb_gtf_tag_exon_parent_gene}"} \\\\
-    \\${par_sjdb_gtf_tag_exon_parent_geneName:+--sjdbGTFtag_exon_parent_geneName "\\${par_sjdb_gtf_tag_exon_parent_geneName}"} \\\\
-    \\${par_sjdb_gtf_tag_exon_parent_geneType:+--sjdbGTFtag_exon_parent_geneType "\\${sjdbGTFtag_exon_parent_geneType}"} \\\\
+    \\${par_sjdb_gtf_tag_exon_parent_transcript:+--sjdbGTFtagExonParentTranscript "\\${par_sjdb_gtf_tag_exon_parent_transcript}"} \\\\
+    \\${par_sjdb_gtf_tag_exon_parent_gene:+--sjdbGTFtagExonParentGene "\\${par_sjdb_gtf_tag_exon_parent_gene}"} \\\\
+    \\${sjdb_gtf_tag_exon_parent_gene_name:+--sjdbGTFtagExonParentGeneName "\\${sjdb_gtf_tag_exon_parent_gene_name}"} \\\\
+    \\${sjdb_gtf_tag_exon_parent_gene_type:+--sjdbGTFtagExonParentGeneType "\\${sjdb_gtf_tag_exon_parent_gene_type}"} \\\\
     \\${par_limit_genome_generate_ram:+--limitGenomeGenerateRAM "\\${par_limit_genome_generate_ram}"} \\\\
     \\${par_genome_chr_bin_nbits:+--genomeChrBinNbits "\\${par_genome_chr_bin_nbits}"} \\\\
     \\${par_genome_sa_sparse_d:+--genomeSAsparseD "\\${par_genome_sa_sparse_d}"} \\\\
@@ -3636,7 +3866,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3650,6 +3880,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/nextflow_schema.json

@@ -187,10 +187,10 @@
                 "index": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.index.index`. STAR index directory",
-                "help_text": "Type: `file`, required, default: `$id.$key.index.index`. STAR index directory."
+                "description": "Type: `file`, required, default: `STAR_index`. STAR index directory",
+                "help_text": "Type: `file`, required, default: `STAR_index`. STAR index directory."
             ,
-                "default":"$id.$key.index.index"
+                "default":"STAR_index"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/trimgalore/.config.vsh.yaml

@@ -668,6 +668,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -769,16 +772,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/trimgalore"
   executable: "target/nextflow/trimgalore/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/trimgalore/main.nf

@@ -1,6 +1,6 @@
 // trimgalore main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3438,6 +3664,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3559,16 +3789,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/trimgalore",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -4138,7 +4368,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -4152,6 +4382,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/trimgalore/nextflow_schema.json

@@ -527,10 +527,10 @@
                 "output_dir": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. If specified all output will be written to this directory instead of the current directory",
-                "help_text": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. If specified all output will be written to this directory instead of the current directory."
+                "description": "Type: `file`, required, default: `trimmed_output`. If specified all output will be written to this directory instead of the current directory",
+                "help_text": "Type: `file`, required, default: `trimmed_output`. If specified all output will be written to this directory instead of the current directory."
             ,
-                "default":"$id.$key.output_dir.output_dir"
+                "default":"trimmed_output"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml

@@ -509,6 +509,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -610,16 +613,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/umi_tools/umi_tools_dedup"
   executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_dedup/main.nf

@@ -1,6 +1,6 @@
 // umi_tools_dedup main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -176,7 +171,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +190,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +204,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1667,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1880,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1892,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1904,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1945,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1965,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +1996,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2006,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2690,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2848,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2890,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2986,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3364,6 +3590,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3486,16 +3716,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_dedup",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -4008,7 +4238,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -4022,6 +4252,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_dedup/nextflow_schema.json

@@ -68,10 +68,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.output.output`. Deduplicated BAM file",
-                "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Deduplicated BAM file."
+                "description": "Type: `file`, required, default: `$id.$key.output`. Deduplicated BAM file",
+                "help_text": "Type: `file`, required, default: `$id.$key.output`. Deduplicated BAM file."
             ,
-                "default":"$id.$key.output.output"
+                "default":"$id.$key.output"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml

@@ -331,6 +331,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -433,16 +436,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/umi_tools/umi_tools_extract"
   executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf

@@ -1,6 +1,6 @@
 // umi_tools_extract main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -173,7 +168,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +187,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +201,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1664,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1877,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1889,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1901,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1942,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1962,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1993,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2003,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2687,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2845,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2887,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2983,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3175,6 +3401,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3298,16 +3528,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_extract",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3809,7 +4039,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3823,6 +4053,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json

@@ -67,10 +67,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.output.output`. Output file for read 1",
-                "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output file for read 1."
+                "description": "Type: `file`, required, default: `$id.$key.output`. Output file for read 1",
+                "help_text": "Type: `file`, required, default: `$id.$key.output`. Output file for read 1."
             ,
-                "default":"$id.$key.output.output"
+                "default":"$id.$key.output"
             }
     
 
@@ -78,10 +78,10 @@
                 "read2_out": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.read2_out.read2_out`. Output file for read 2",
-                "help_text": "Type: `file`, default: `$id.$key.read2_out.read2_out`. Output file for read 2."
+                "description": "Type: `file`, default: `$id.$key.read2_out`. Output file for read 2",
+                "help_text": "Type: `file`, default: `$id.$key.read2_out`. Output file for read 2."
             ,
-                "default":"$id.$key.read2_out.read2_out"
+                "default":"$id.$key.read2_out"
             }
     
 
@@ -269,10 +269,10 @@
                 "log": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.log.log`. File with logging information",
-                "help_text": "Type: `file`, default: `$id.$key.log.log`. File with logging information."
+                "description": "Type: `file`, default: `$id.$key.log`. File with logging information",
+                "help_text": "Type: `file`, default: `$id.$key.log`. File with logging information."
             ,
-                "default":"$id.$key.log.log"
+                "default":"$id.$key.log"
             }
     
 
@@ -301,10 +301,10 @@
                 "error": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.error.error`. File with error information",
-                "help_text": "Type: `file`, default: `$id.$key.error.error`. File with error information."
+                "description": "Type: `file`, default: `$id.$key.error`. File with error information",
+                "help_text": "Type: `file`, default: `$id.$key.error`. File with error information."
             ,
-                "default":"$id.$key.error.error"
+                "default":"$id.$key.error"
             }
     
 
@@ -332,10 +332,10 @@
                 "timeit": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.timeit.timeit`. Store timing information in file",
-                "help_text": "Type: `file`, default: `$id.$key.timeit.timeit`. Store timing information in file."
+                "description": "Type: `file`, default: `$id.$key.timeit`. Store timing information in file",
+                "help_text": "Type: `file`, default: `$id.$key.timeit`. Store timing information in file."
             ,
-                "default":"$id.$key.timeit.timeit"
+                "default":"$id.$key.timeit"
             }
     
 

target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml

@@ -153,6 +153,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -255,16 +258,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/umi_tools/umi_tools_prepareforrsem"
   executable: "target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf

@@ -1,6 +1,6 @@
 // umi_tools_prepareforrsem main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -173,7 +168,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +187,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +201,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1664,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // 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]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // 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 [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // 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 filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1877,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1889,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1901,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-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 '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1942,10 @@ 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, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] 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.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1962,7 @@ 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, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1993,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2003,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          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, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2687,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2845,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2887,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2983,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2997,6 +3223,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3120,16 +3350,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_prepareforrsem",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3562,7 +3792,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3576,6 +3806,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_prepareforrsem/nextflow_schema.json

@@ -48,10 +48,10 @@
                 "log": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.log.log`. File with logging information [default = stdout]",
-                "help_text": "Type: `file`, default: `$id.$key.log.log`. File with logging information [default = stdout]."
+                "description": "Type: `file`, default: `$id.$key.log`. File with logging information [default = stdout]",
+                "help_text": "Type: `file`, default: `$id.$key.log`. File with logging information [default = stdout]."
             ,
-                "default":"$id.$key.log.log"
+                "default":"$id.$key.log"
             }
     
 
@@ -59,10 +59,10 @@
                 "error": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.error.error`. File with error information [default = stderr]",
-                "help_text": "Type: `file`, default: `$id.$key.error.error`. File with error information [default = stderr]."
+                "description": "Type: `file`, default: `$id.$key.error`. File with error information [default = stderr]",
+                "help_text": "Type: `file`, default: `$id.$key.error`. File with error information [default = stderr]."
             ,
-                "default":"$id.$key.error.error"
+                "default":"$id.$key.error"
             }
     
 

target/executable/bedtools_genomecov/.config.vsh.yaml

@@ -80,6 +80,9 @@ info:
     - "modules/local/bedtools_genomecov.nf"
     last_sha: "0a1bdcfbb498987643b74e9fccab85ccd9f2a17d"
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -182,15 +185,15 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bedtools_genomecov"
   executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
-  viash_version: "0.9.0"
-  git_commit: "2b3d511b34246648b934fd1dc99b22e0a71c37f2"
-  git_remote: "https://x-access-token:ghs_mpjpezoXRPhvITbEzvFPaxzcp8yfML2ITu9P@github.com/viash-hub/rnaseq"
+  viash_version: "0.9.2"
+  git_commit: "f52978a0e25cae182b7874b4b8aa3afc183e880e"
+  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
   info:
     test_resources:
-    - path: "gs://viash-hub-test-data/rnaseq/v1"
+    - path: "gs://viash-hub-resources/rnaseq/v1"
       dest: "testData"
   repositories:
   - type: "vsh"
@@ -201,7 +204,7 @@ package_config:
     name: "craftbox"
     repo: "craftbox"
     tag: "v0.1.0"
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:

target/executable/bedtools_genomecov/bedtools_genomecov

@@ -2,7 +2,7 @@
 
 # bedtools_genomecov main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,35 +169,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bedtools_genomecov main"
-  echo ""
-  echo "Compute BEDGRAPH (-bg) summaries of feature coverage"
-  echo ""
-  echo "Input:"
-  echo "    --strandedness"
-  echo "        type: string"
-  echo "        choices: [ unstranded, forward, reverse, auto ]"
-  echo "        Sample strand-specificity."
-  echo ""
-  echo "    --bam"
-  echo "        type: file, file must exist"
-  echo "        Genome BAM file"
-  echo ""
-  echo "    --extra_bedtools_args"
-  echo "        type: string"
-  echo "        default:"
-  echo ""
-  echo "Output:"
-  echo "    --bedgraph_forward"
-  echo "        type: file, output, file must exist"
-  echo "        default: \$id.forward.bedgraph"
-  echo ""
-  echo "    --bedgraph_reverse"
-  echo "        type: file, output, file must exist"
-  echo "        default: \$id.reverse.bedgraph"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -481,9 +452,9 @@ mv bedtools.static /usr/local/bin/bedtools && \
 chmod a+x /usr/local/bin/bedtools
 
 LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
-LABEL org.opencontainers.image.created="2024-12-05T14:40:12Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_mpjpezoXRPhvITbEzvFPaxzcp8yfML2ITu9P@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="2b3d511b34246648b934fd1dc99b22e0a71c37f2"
+LABEL org.opencontainers.image.created="2025-05-06T19:18:33Z"
+LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="f52978a0e25cae182b7874b4b8aa3afc183e880e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -598,6 +569,61 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bedtools_genomecov main"
+  echo ""
+  echo "Compute BEDGRAPH (-bg) summaries of feature coverage"
+  echo ""
+  echo "Input:"
+  echo "    --strandedness"
+  echo "        type: string"
+  echo "        choices: [ unstranded, forward, reverse, auto ]"
+  echo "        Sample strand-specificity."
+  echo ""
+  echo "    --bam"
+  echo "        type: file, file must exist"
+  echo "        Genome BAM file"
+  echo ""
+  echo "    --extra_bedtools_args"
+  echo "        type: string"
+  echo "        default:"
+  echo ""
+  echo "Output:"
+  echo "    --bedgraph_forward"
+  echo "        type: file, output, file must exist"
+  echo "        default: \$id.forward.bedgraph"
+  echo ""
+  echo "    --bedgraph_reverse"
+  echo "        type: file, output, file must exist"
+  echo "        default: \$id.reverse.bedgraph"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 

target/executable/cat_additional_fasta/.config.vsh.yaml

@@ -90,6 +90,9 @@ info:
     - "modules/local/cat_additional_fasta.nf"
     last_sha: "0a1bdcfbb498987643b74e9fccab85ccd9f2a17d"
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -186,15 +189,15 @@ build_info:
   engine: "docker|native"
   output: "target/executable/cat_additional_fasta"
   executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
-  viash_version: "0.9.0"
-  git_commit: "2b3d511b34246648b934fd1dc99b22e0a71c37f2"
-  git_remote: "https://x-access-token:ghs_mpjpezoXRPhvITbEzvFPaxzcp8yfML2ITu9P@github.com/viash-hub/rnaseq"
+  viash_version: "0.9.2"
+  git_commit: "f52978a0e25cae182b7874b4b8aa3afc183e880e"
+  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
   info:
     test_resources:
-    - path: "gs://viash-hub-test-data/rnaseq/v1"
+    - path: "gs://viash-hub-resources/rnaseq/v1"
       dest: "testData"
   repositories:
   - type: "vsh"
@@ -205,7 +208,7 @@ package_config:
     name: "craftbox"
     repo: "craftbox"
     tag: "v0.1.0"
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:

target/executable/cat_additional_fasta/cat_additional_fasta

@@ -2,7 +2,7 @@
 
 # cat_additional_fasta main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,40 +169,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "cat_additional_fasta main"
-  echo ""
-  echo "Concatenate addional fasta file to reference FASTA and GTF files."
-  echo ""
-  echo "Input:"
-  echo "    --fasta"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Path to FASTA genome file."
-  echo ""
-  echo "    --gtf"
-  echo "        type: file, file must exist"
-  echo "        Path to GTF annotation file."
-  echo ""
-  echo "    --additional_fasta"
-  echo "        type: file, file must exist"
-  echo "        FASTA file to concatenate to genome FASTA file e.g. containing spike-in"
-  echo "        sequences."
-  echo ""
-  echo "    --biotype"
-  echo "        type: string"
-  echo "        Biotype value to use when appending entries to GTF file when additional"
-  echo "        fasta file is provided."
-  echo ""
-  echo "Output:"
-  echo "    --fasta_output"
-  echo "        type: file, output, file must exist"
-  echo "        Concatenated FASTA file."
-  echo ""
-  echo "    --gtf_output"
-  echo "        type: file, output, file must exist"
-  echo "        Concatenated GTF file."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -480,9 +446,9 @@ function ViashDockerfile {
 FROM python:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
-LABEL org.opencontainers.image.created="2024-12-05T14:40:11Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_mpjpezoXRPhvITbEzvFPaxzcp8yfML2ITu9P@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="2b3d511b34246648b934fd1dc99b22e0a71c37f2"
+LABEL org.opencontainers.image.created="2025-05-06T19:18:34Z"
+LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="f52978a0e25cae182b7874b4b8aa3afc183e880e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -597,6 +563,66 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "cat_additional_fasta main"
+  echo ""
+  echo "Concatenate addional fasta file to reference FASTA and GTF files."
+  echo ""
+  echo "Input:"
+  echo "    --fasta"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Path to FASTA genome file."
+  echo ""
+  echo "    --gtf"
+  echo "        type: file, file must exist"
+  echo "        Path to GTF annotation file."
+  echo ""
+  echo "    --additional_fasta"
+  echo "        type: file, file must exist"
+  echo "        FASTA file to concatenate to genome FASTA file e.g. containing spike-in"
+  echo "        sequences."
+  echo ""
+  echo "    --biotype"
+  echo "        type: string"
+  echo "        Biotype value to use when appending entries to GTF file when additional"
+  echo "        fasta file is provided."
+  echo ""
+  echo "Output:"
+  echo "    --fasta_output"
+  echo "        type: file, output, file must exist"
+  echo "        Concatenated FASTA file."
+  echo ""
+  echo "    --gtf_output"
+  echo "        type: file, output, file must exist"
+  echo "        Concatenated GTF file."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 

target/executable/cat_fastq/.config.vsh.yaml

@@ -77,6 +77,9 @@ info:
     - "modules/nf-core/cat/fastq/meta.yml"
     last_sha: "54721c6946daf6d602d7069dc127deef9cbe6b33"
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -173,15 +176,15 @@ build_info:
   engine: "docker|native"
   output: "target/executable/cat_fastq"
   executable: "target/executable/cat_fastq/cat_fastq"
-  viash_version: "0.9.0"
-  git_commit: "2b3d511b34246648b934fd1dc99b22e0a71c37f2"
-  git_remote: "https://x-access-token:ghs_mpjpezoXRPhvITbEzvFPaxzcp8yfML2ITu9P@github.com/viash-hub/rnaseq"
+  viash_version: "0.9.2"
+  git_commit: "f52978a0e25cae182b7874b4b8aa3afc183e880e"
+  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
   info:
     test_resources:
-    - path: "gs://viash-hub-test-data/rnaseq/v1"
+    - path: "gs://viash-hub-resources/rnaseq/v1"
       dest: "testData"
   repositories:
   - type: "vsh"
@@ -192,7 +195,7 @@ package_config:
     name: "craftbox"
     repo: "craftbox"
     tag: "v0.1.0"
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:

target/executable/cat_fastq/cat_fastq

@@ -2,7 +2,7 @@
 
 # cat_fastq main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,32 +169,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "cat_fastq main"
-  echo ""
-  echo "Concatenate multiple fastq files"
-  echo ""
-  echo "Input:"
-  echo "    --read_1"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        Read 1 fastq files to be concatenated"
-  echo ""
-  echo "    --read_2"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        Read 2 fastq files to be concatenated"
-  echo ""
-  echo "Output:"
-  echo "    --fastq_1"
-  echo "        type: file, output, file must exist"
-  echo "        default: \$id_r1.fastq"
-  echo "        Concatenated read 1 fastq"
-  echo ""
-  echo "    --fastq_2"
-  echo "        type: file, output"
-  echo "        default: \$id_r2.fastq"
-  echo "        Concatenated read 2 fastq"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -472,9 +446,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
-LABEL org.opencontainers.image.created="2024-12-05T14:40:10Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_mpjpezoXRPhvITbEzvFPaxzcp8yfML2ITu9P@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="2b3d511b34246648b934fd1dc99b22e0a71c37f2"
+LABEL org.opencontainers.image.created="2025-05-06T19:18:31Z"
+LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="f52978a0e25cae182b7874b4b8aa3afc183e880e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -589,6 +563,58 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "cat_fastq main"
+  echo ""
+  echo "Concatenate multiple fastq files"
+  echo ""
+  echo "Input:"
+  echo "    --read_1"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        Read 1 fastq files to be concatenated"
+  echo ""
+  echo "    --read_2"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        Read 2 fastq files to be concatenated"
+  echo ""
+  echo "Output:"
+  echo "    --fastq_1"
+  echo "        type: file, output, file must exist"
+  echo "        default: \$id_r1.fastq"
+  echo "        Concatenated read 1 fastq"
+  echo ""
+  echo "    --fastq_2"
+  echo "        type: file, output"
+  echo "        default: \$id_r2.fastq"
+  echo "        Concatenated read 2 fastq"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 

target/executable/copy_if_exists/.config.vsh.yaml

@@ -0,0 +1,183 @@
+name: "copy_if_exists"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--required_file"
+    info: null
+    example:
+    - "/tmp/rnaseq_workflow_config/required_file.txt"
+    must_exist: false
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--optional_file"
+    info: null
+    example:
+    - "/tmp/rnaseq_workflow_config/optional_file.txt"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Ouput"
+  arguments:
+  - type: "file"
+    name: "--output"
+    info: null
+    default:
+    - "copy_if_exists_output"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+- type: "file"
+  path: "required_file.txt"
+- type: "file"
+  path: "optional_file.txt"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "biobox"
+  tag: "main"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "ubuntu:22.04"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/extra/copy_if_exists/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/copy_if_exists"
+  executable: "target/executable/copy_if_exists/copy_if_exists"
+  viash_version: "0.9.2"
+  git_commit: "f52978a0e25cae182b7874b4b8aa3afc183e880e"
+  git_remote: "https://github.com/viash-hub/rnaseq"
+package_config:
+  name: "rnaseq"
+  version: "main"
+  info:
+    test_resources:
+    - path: "gs://viash-hub-resources/rnaseq/v1"
+      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "biobox"
+    tag: "main"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
+  viash_version: "0.9.2"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n.resources += {path: '/src/workflows/utils/labels.config',\
+    \ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
+    \ := '$id'\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  organization: "vsh"

target/executable/copy_if_exists/nextflow_labels.config

@@ -0,0 +1,44 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 2 }
+  withLabel: midcpu { cpus = 4 }
+  withLabel: highcpu { cpus = 8 }
+  withLabel: veryhighcpu { cpus = 16 }
+ 
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 48.GB * task.attempt ) } }
+}
+
+def get_memory(to_compare) {
+  if (!process.containsKey("maxMemory") || !process.maxMemory) {
+    return to_compare
+  }
+
+  try {
+    if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+      return process.maxMemory
+    }
+    else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+      return max_memory as nextflow.util.MemoryUnit
+    }
+    else {
+      return to_compare
+    }
+  } catch (all) {
+        println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}
+

target/executable/copy_if_exists/optional_file.txt

@@ -0,0 +1 @@
+Optional!

target/executable/copy_if_exists/required_file.txt

@@ -0,0 +1 @@
+Required!

target/executable/deseq2_qc/.config.vsh.yaml

@@ -133,6 +133,9 @@ info:
     - "modules/local/deseq2_qc.nf"
     last_sha: "92b2a7857de1dda9d1c19a088941fc81e2976ff7"
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -215,11 +218,20 @@ runners:
 engines:
 - type: "docker"
   id: "docker"
-  image: "rocker/r2u:22.04"
+  image: "debian:latest"
   target_registry: "images.viash-hub.com"
   target_tag: "main"
   namespace_separator: "/"
   setup:
+  - type: "apt"
+    packages:
+    - "libcurl4-openssl-dev"
+    - "r-base"
+    - "r-base-core"
+    - "libxml2-dev"
+    - "procps"
+    - "libssl-dev"
+    interactive: false
   - type: "r"
     cran:
     - "optparse"
@@ -231,6 +243,7 @@ engines:
     bioc:
     - "DESeq2"
     bioc_force_install: false
+    warnings_as_errors: true
   entrypoint: []
   cmd: null
 - type: "native"
@@ -241,15 +254,15 @@ build_info:
   engine: "docker|native"
   output: "target/executable/deseq2_qc"
   executable: "target/executable/deseq2_qc/deseq2_qc"
-  viash_version: "0.9.0"
-  git_commit: "2b3d511b34246648b934fd1dc99b22e0a71c37f2"
-  git_remote: "https://x-access-token:ghs_mpjpezoXRPhvITbEzvFPaxzcp8yfML2ITu9P@github.com/viash-hub/rnaseq"
+  viash_version: "0.9.2"
+  git_commit: "f52978a0e25cae182b7874b4b8aa3afc183e880e"
+  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"
   info:
     test_resources:
-    - path: "gs://viash-hub-test-data/rnaseq/v1"
+    - path: "gs://viash-hub-resources/rnaseq/v1"
       dest: "testData"
   repositories:
   - type: "vsh"
@@ -260,7 +273,7 @@ package_config:
     name: "craftbox"
     repo: "craftbox"
     tag: "v0.1.0"
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods: