Build branch v0.1 with version v0.1.1 (5ad947d)

Build pipeline: viash-hub.demultiplex.v0.1-s7dfp Source commit: 5ad947dd1e Source message: Re-release v0.1.1
Build branch v0.1 with version v0.1.1 (ff28cec)
2024-09-13 10:05:59 +00:00 · 2024-09-12 15:52:47 +00:00
37 changed files with 924 additions and 453 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,8 @@
 target
 testData
+test_resources

 # Nextflow related files
 .nextflow
 .nextflow.log*
-work
+work
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,17 +1,13 @@
-# 0.1.2
+# v0.1.1

-## NEW FEATURES
+## Minor updates
+
+* Bump viash to 0.9.0 (PR #14).
+
+* `demultiplex` workflow: use `v0.2.0` release instead of `main` branch for `biobox` dependencies (PR #11).

 * Renamed `biobase` repository to `biobox` (PR #13 and PR #15).

-* Bump viash to 0.9.0-RC6 (PR #14).
-
-# v0.1.1
-
-## NEW FEATURES
-
-* `demultiplex` workflow: use `v0.1.0` release instead of `main` branch for `biobase` dependencies (PR #11).
-
 # v0.1.0

-Initial release
+Initial release
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 name: demultiplex
-version: v0.1.0
+version: v0.1.1
 description: |
  Demultiplexing pipeline
 license: MIT
@@ -12,7 +12,7 @@ info:
    - path: https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz
      dest: test_resources

-viash_version: 0.9.0-RC6
+viash_version: 0.9.0

 config_mods: |
  .requirements.commands := ['ps']
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,6 +1,6 @@
 manifest {
  name = "demultiplex"
-  version = "v0.1.0"
+  version = "v0.1.1"
  defaultBranch = "main"
  nextflowVersion = "!>=20.12.1-edge"
 }
--- a/src/demultiplex/config.vsh.yaml
+++ b/src/demultiplex/config.vsh.yaml
@@ -61,7 +61,7 @@ repositories:
  - name: bb
    type: vsh
    repo: biobox
-    tag: v0.1.0
+    tag: v0.2.0

 runners:
  - type: nextflow
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/.config.vsh.yaml
@@ -1,5 +1,30 @@
 name: "bcl_convert"
-version: "v0.1.0"
+version: "0.2.0"
+authors:
+- name: "Toni Verbeiren"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      github: "tverbeiren"
+      linkedin: "verbeiren"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist and CEO"
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  info:
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -281,9 +306,16 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
-license: "MIT"
+keywords:
+- "demultiplex"
+- "fastq"
+- "bcl"
+- "illumina"
+license: "Proprietary"
 links:
  repository: "https://github.com/viash-hub/biobox"
+  homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html"
+  documentation: "https://support.illumina.com/downloads/bcl-convert-user-guide.html"
 runners:
 - type: "executable"
  id: "executable"
@@ -354,7 +386,7 @@ engines:
  id: "docker"
  image: "debian:trixie-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "0.2.0"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -385,22 +417,22 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/bcl_convert"
  executable: "target/nextflow/bcl_convert/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724"
+  viash_version: "0.9.0"
+  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "v0.1.0"
+  version: "0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/main.nf
@@ -1,13 +1,17 @@
-// bcl_convert v0.1.0
+// bcl_convert 0.2.0
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
 // files, or include a separate license file detailing the licenses of all included
 // files.
+// 
+// Component authors:
+//  * Toni Verbeiren (author, maintainer)
+//  * Dorien Roosen (author)

 ////////////////////////////
 // VDSL3 helper functions //
@@ -760,8 +764,11 @@ def runEach(Map args) {
  def fromState_ = args.fromState
  def toState_ = args.toState
  def filter_ = args.filter
+  def runIf_ = args.runIf
  def id_ = args.id

+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
  workflow runEachWf {
    take: input_ch
    main:
@@ -783,7 +790,20 @@ def runEach(Map args) {
          [new_id] + tup.drop(1)
        }
        : filter_ch
-      def data_ch = id_ch | map{tup ->
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
          def new_data = tup[1]
          if (fromState_ instanceof Map) {
            new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +841,11 @@ def runEach(Map args) {
          [tup[0], new_state] + tup.drop(3)
        }
        : out_ch
+
+      def return_ch = post_ch
+        | concat(chPassthrough)
      
-      post_ch
+      return_ch
    }

    // mix all results
@@ -1598,8 +1621,8 @@ def findStates(Map params, Map config) {
          // construct renameMap
          if (args.rename_keys) {
            def renameMap = args.rename_keys.collectEntries{renameString ->
-              def split = renameString.split(";")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
              split
            }

@@ -1709,7 +1732,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1805,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .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
@@ -1822,7 +1849,9 @@ def publishStatesByConfig(Map args) {
                // 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
@@ -2626,30 +2655,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
        tuple
      }

-    def chModifiedFiltered = workflowArgs.filter ?
-      chModified | filter{workflowArgs.filter(it)} :
-      chModified

    def chRun = null
    def chPassthrough = null
    if (workflowArgs.runIf) {
-      def runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModified.branch{ tup ->
        run: workflowArgs.runIf(tup[0], tup[1])
        passthrough: true
      }
      chRun = runIfBranch.run
      chPassthrough = runIfBranch.passthrough
    } else {
-      chRun = chModifiedFiltered
+      chRun = chModified
      chPassthrough = Channel.empty()
    }

+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
    def chArgs = workflowArgs.fromState ? 
-      chRun | map{
+      chRunFiltered | map{
        def new_data = workflowArgs.fromState(it.take(2))
        [it[0], new_data]
      } :
-      chRun | map {tup -> tup.take(2)}
+      chRunFiltered | map {tup -> tup.take(2)}

    // fill in defaults
    def chArgsWithDefaults = chArgs
@@ -2720,7 +2750,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
      // | view{"chInitialOutput: ${it.take(3)}"}

    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
      // input tuple format: [join_id, id, output, prev_state, ...]
      // output tuple format: [join_id, id, new_state, ...]
      | map{ tup ->
@@ -2779,7 +2809,49 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "bcl_convert",
-  "version" : "v0.1.0",
+  "version" : "0.2.0",
+  "authors" : [
+    {
+      "name" : "Toni Verbeiren",
+      "roles" : [
+        "author",
+        "maintainer"
+      ],
+      "info" : {
+        "links" : {
+          "github" : "tverbeiren",
+          "linkedin" : "verbeiren"
+        },
+        "organizations" : [
+          {
+            "name" : "Data Intuitive",
+            "href" : "https://www.data-intuitive.com",
+            "role" : "Data Scientist and CEO"
+          }
+        ]
+      }
+    },
+    {
+      "name" : "Dorien Roosen",
+      "roles" : [
+        "author"
+      ],
+      "info" : {
+        "links" : {
+          "email" : "dorien@data-intuitive.com",
+          "github" : "dorien-er",
+          "linkedin" : "dorien-roosen"
+        },
+        "organizations" : [
+          {
+            "name" : "Data Intuitive",
+            "href" : "https://www.data-intuitive.com",
+            "role" : "Data Scientist"
+          }
+        ]
+      }
+    }
+  ],
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3125,9 +3197,17 @@ meta = [
      "ps"
    ]
  },
-  "license" : "MIT",
+  "keywords" : [
+    "demultiplex",
+    "fastq",
+    "bcl",
+    "illumina"
+  ],
+  "license" : "Proprietary",
  "links" : {
-    "repository" : "https://github.com/viash-hub/biobox"
+    "repository" : "https://github.com/viash-hub/biobox",
+    "homepage" : "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html",
+    "documentation" : "https://support.illumina.com/downloads/bcl-convert-user-guide.html"
  },
  "runners" : [
    {
@@ -3209,7 +3289,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:trixie-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3248,22 +3328,22 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/bcl_convert",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "b84b29747d0635f2ac83ea63b496be9a9edb6724",
+    "viash_version" : "0.9.0",
+    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
    "git_remote" : "https://github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "v0.1.0",
+    "version" : "0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := '0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3454,7 +3534,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
              val = val.join(par.multiple_sep)
            }
            if (par.direction == "output" && par.type == "file") {
-              val = val.replaceAll('\\$id', id).replaceAll('\\$key', key)
+              val = val
+                .replaceAll('\\$id', id)
+                .replaceAll('\\$\\{id\\}', id)
+                .replaceAll('\\$key', key)
+                .replaceAll('\\$\\{key\\}', key)
            }
            [parName, val]
          }
@@ -3585,7 +3669,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def createParentStr = meta.config.allArguments
    .findAll { it.type == "file" && it.direction == "output" && it.create_parent }
    .collect { par -> 
-      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
+      def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]"
+      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }"
    }
    .join("\n")

@@ -3593,8 +3678,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def inputFileExports = meta.config.allArguments
    .findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
    .collect { par ->
-      def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
-      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
+      def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}"
+      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}"
    }

  // NOTE: if using docker, use /tmp instead of tmpDir!
@@ -3631,6 +3716,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def procStr = 
  """nextflow.enable.dsl=2
  |
+  |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") }
  |process $procKey {$drctvStrs
  |input:
  |  tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3642,10 +3728,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  |$stub
  |\"\"\"
  |script:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
  |def parInject = args
  |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
  |  .join("\\n")
  |\"\"\"
  |# meta exports
@@ -3730,7 +3815,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/bcl_convert",
-    "tag" : "v0.1.0"
+    "tag" : "0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/nextflow.config
@@ -2,8 +2,9 @@ manifest {
  name = 'bcl_convert'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = '0.2.0'
  description = 'Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\nand [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n'
+  author = 'Toni Verbeiren, Dorien Roosen'
 }

 process.container = 'nextflow/bash:latest'
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/nextflow_schema.json
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/nextflow_schema.json
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/.config.vsh.yaml
@@ -1,5 +1,18 @@
 name: "falco"
-version: "v0.1.0"
+version: "0.2.0"
+authors:
+- name: "Toni Verbeiren"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      github: "tverbeiren"
+      linkedin: "verbeiren"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist and CEO"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -274,7 +287,7 @@ engines:
  id: "docker"
  image: "debian:trixie-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "0.2.0"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -303,22 +316,22 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/falco"
  executable: "target/nextflow/falco/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724"
+  viash_version: "0.9.0"
+  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "v0.1.0"
+  version: "0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/main.nf
@@ -1,13 +1,16 @@
-// falco v0.1.0
+// falco 0.2.0
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
 // files, or include a separate license file detailing the licenses of all included
 // files.
+// 
+// Component authors:
+//  * Toni Verbeiren (author, maintainer)

 ////////////////////////////
 // VDSL3 helper functions //
@@ -760,8 +763,11 @@ def runEach(Map args) {
  def fromState_ = args.fromState
  def toState_ = args.toState
  def filter_ = args.filter
+  def runIf_ = args.runIf
  def id_ = args.id

+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
  workflow runEachWf {
    take: input_ch
    main:
@@ -783,7 +789,20 @@ def runEach(Map args) {
          [new_id] + tup.drop(1)
        }
        : filter_ch
-      def data_ch = id_ch | map{tup ->
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
          def new_data = tup[1]
          if (fromState_ instanceof Map) {
            new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +840,11 @@ def runEach(Map args) {
          [tup[0], new_state] + tup.drop(3)
        }
        : out_ch
+
+      def return_ch = post_ch
+        | concat(chPassthrough)
      
-      post_ch
+      return_ch
    }

    // mix all results
@@ -1598,8 +1620,8 @@ def findStates(Map params, Map config) {
          // construct renameMap
          if (args.rename_keys) {
            def renameMap = args.rename_keys.collectEntries{renameString ->
-              def split = renameString.split(";")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
              split
            }

@@ -1709,7 +1731,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1804,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .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
@@ -1822,7 +1848,9 @@ def publishStatesByConfig(Map args) {
                // 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
@@ -2626,30 +2654,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
        tuple
      }

-    def chModifiedFiltered = workflowArgs.filter ?
-      chModified | filter{workflowArgs.filter(it)} :
-      chModified

    def chRun = null
    def chPassthrough = null
    if (workflowArgs.runIf) {
-      def runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModified.branch{ tup ->
        run: workflowArgs.runIf(tup[0], tup[1])
        passthrough: true
      }
      chRun = runIfBranch.run
      chPassthrough = runIfBranch.passthrough
    } else {
-      chRun = chModifiedFiltered
+      chRun = chModified
      chPassthrough = Channel.empty()
    }

+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
    def chArgs = workflowArgs.fromState ? 
-      chRun | map{
+      chRunFiltered | map{
        def new_data = workflowArgs.fromState(it.take(2))
        [it[0], new_data]
      } :
-      chRun | map {tup -> tup.take(2)}
+      chRunFiltered | map {tup -> tup.take(2)}

    // fill in defaults
    def chArgsWithDefaults = chArgs
@@ -2720,7 +2749,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
      // | view{"chInitialOutput: ${it.take(3)}"}

    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
      // input tuple format: [join_id, id, output, prev_state, ...]
      // output tuple format: [join_id, id, new_state, ...]
      | map{ tup ->
@@ -2779,7 +2808,29 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "falco",
-  "version" : "v0.1.0",
+  "version" : "0.2.0",
+  "authors" : [
+    {
+      "name" : "Toni Verbeiren",
+      "roles" : [
+        "author",
+        "maintainer"
+      ],
+      "info" : {
+        "links" : {
+          "github" : "tverbeiren",
+          "linkedin" : "verbeiren"
+        },
+        "organizations" : [
+          {
+            "name" : "Data Intuitive",
+            "href" : "https://www.data-intuitive.com",
+            "role" : "Data Scientist and CEO"
+          }
+        ]
+      }
+    }
+  ],
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -3080,7 +3131,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:trixie-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3118,22 +3169,22 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/falco",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "b84b29747d0635f2ac83ea63b496be9a9edb6724",
+    "viash_version" : "0.9.0",
+    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
    "git_remote" : "https://github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "v0.1.0",
+    "version" : "0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := '0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3298,7 +3349,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
              val = val.join(par.multiple_sep)
            }
            if (par.direction == "output" && par.type == "file") {
-              val = val.replaceAll('\\$id', id).replaceAll('\\$key', key)
+              val = val
+                .replaceAll('\\$id', id)
+                .replaceAll('\\$\\{id\\}', id)
+                .replaceAll('\\$key', key)
+                .replaceAll('\\$\\{key\\}', key)
            }
            [parName, val]
          }
@@ -3429,7 +3484,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def createParentStr = meta.config.allArguments
    .findAll { it.type == "file" && it.direction == "output" && it.create_parent }
    .collect { par -> 
-      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
+      def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]"
+      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }"
    }
    .join("\n")

@@ -3437,8 +3493,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def inputFileExports = meta.config.allArguments
    .findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
    .collect { par ->
-      def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
-      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
+      def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}"
+      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}"
    }

  // NOTE: if using docker, use /tmp instead of tmpDir!
@@ -3475,6 +3531,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def procStr = 
  """nextflow.enable.dsl=2
  |
+  |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") }
  |process $procKey {$drctvStrs
  |input:
  |  tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3486,10 +3543,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  |$stub
  |\"\"\"
  |script:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
  |def parInject = args
  |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
  |  .join("\\n")
  |\"\"\"
  |# meta exports
@@ -3574,7 +3630,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/falco",
-    "tag" : "v0.1.0"
+    "tag" : "0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/nextflow.config
@@ -2,8 +2,9 @@ manifest {
  name = 'falco'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = '0.2.0'
  description = 'A C++ drop-in replacement of FastQC to assess the quality of sequence read data'
+  author = 'Toni Verbeiren'
 }

 process.container = 'nextflow/bash:latest'
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/nextflow_schema.json
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/nextflow_schema.json
@@ -17,8 +17,8 @@
                "input": {
                "type":
                "string",
-                "description": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\":\"`. input fastq files",
-                "help_text": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\":\"`. input fastq files"
+                "description": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\";\"`. input fastq files",
+                "help_text": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\";\"`. input fastq files"
            
            }
    
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/.config.vsh.yaml
@@ -1,5 +1,19 @@
 name: "multiqc"
-version: "v0.1.0"
+version: "0.2.0"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
 argument_groups:
 - name: "Input"
  arguments:
@@ -63,39 +77,43 @@ argument_groups:
    description: "Use only these module"
    info: null
    example:
-    - "fastqc,cutadapt"
+    - "fastqc"
+    - "cutadapt"
    required: false
    direction: "input"
    multiple: true
-    multiple_sep: ","
+    multiple_sep: ";"
  - type: "string"
    name: "--exclude_modules"
    description: "Do not use only these modules"
    info: null
    example:
-    - "fastqc,cutadapt"
+    - "fastqc"
+    - "cutadapt"
    required: false
    direction: "input"
    multiple: true
-    multiple_sep: ","
+    multiple_sep: ";"
  - type: "string"
    name: "--ignore_analysis"
    info: null
    example:
-    - "run_one/*,run_two/*"
+    - "run_one/*"
+    - "run_two/*"
    required: false
    direction: "input"
    multiple: true
-    multiple_sep: ","
+    multiple_sep: ";"
  - type: "string"
    name: "--ignore_samples"
    info: null
    example:
-    - "sample_1*,sample_3*"
+    - "sample_1*"
+    - "sample_3*"
    required: false
    direction: "input"
    multiple: true
-    multiple_sep: ","
+    multiple_sep: ";"
  - type: "boolean_true"
    name: "--ignore_symlinks"
    description: "Ignore symlinked directories and files"
@@ -415,7 +433,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -437,22 +455,22 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/multiqc"
  executable: "target/nextflow/multiqc/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724"
+  viash_version: "0.9.0"
+  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "v0.1.0"
+  version: "0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf
@@ -1,13 +1,16 @@
-// multiqc v0.1.0
+// multiqc 0.2.0
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
 // files, or include a separate license file detailing the licenses of all included
 // files.
+// 
+// Component authors:
+//  * Dorien Roosen (author, maintainer)

 ////////////////////////////
 // VDSL3 helper functions //
@@ -760,8 +763,11 @@ def runEach(Map args) {
  def fromState_ = args.fromState
  def toState_ = args.toState
  def filter_ = args.filter
+  def runIf_ = args.runIf
  def id_ = args.id

+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
  workflow runEachWf {
    take: input_ch
    main:
@@ -783,7 +789,20 @@ def runEach(Map args) {
          [new_id] + tup.drop(1)
        }
        : filter_ch
-      def data_ch = id_ch | map{tup ->
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
          def new_data = tup[1]
          if (fromState_ instanceof Map) {
            new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +840,11 @@ def runEach(Map args) {
          [tup[0], new_state] + tup.drop(3)
        }
        : out_ch
+
+      def return_ch = post_ch
+        | concat(chPassthrough)
      
-      post_ch
+      return_ch
    }

    // mix all results
@@ -1598,8 +1620,8 @@ def findStates(Map params, Map config) {
          // construct renameMap
          if (args.rename_keys) {
            def renameMap = args.rename_keys.collectEntries{renameString ->
-              def split = renameString.split(";")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
              split
            }

@@ -1709,7 +1731,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1804,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .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
@@ -1822,7 +1848,9 @@ def publishStatesByConfig(Map args) {
                // 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
@@ -2626,30 +2654,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
        tuple
      }

-    def chModifiedFiltered = workflowArgs.filter ?
-      chModified | filter{workflowArgs.filter(it)} :
-      chModified

    def chRun = null
    def chPassthrough = null
    if (workflowArgs.runIf) {
-      def runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModified.branch{ tup ->
        run: workflowArgs.runIf(tup[0], tup[1])
        passthrough: true
      }
      chRun = runIfBranch.run
      chPassthrough = runIfBranch.passthrough
    } else {
-      chRun = chModifiedFiltered
+      chRun = chModified
      chPassthrough = Channel.empty()
    }

+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
    def chArgs = workflowArgs.fromState ? 
-      chRun | map{
+      chRunFiltered | map{
        def new_data = workflowArgs.fromState(it.take(2))
        [it[0], new_data]
      } :
-      chRun | map {tup -> tup.take(2)}
+      chRunFiltered | map {tup -> tup.take(2)}

    // fill in defaults
    def chArgsWithDefaults = chArgs
@@ -2720,7 +2749,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
      // | view{"chInitialOutput: ${it.take(3)}"}

    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
      // input tuple format: [join_id, id, output, prev_state, ...]
      // output tuple format: [join_id, id, new_state, ...]
      | map{ tup ->
@@ -2779,7 +2808,30 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "multiqc",
-  "version" : "v0.1.0",
+  "version" : "0.2.0",
+  "authors" : [
+    {
+      "name" : "Dorien Roosen",
+      "roles" : [
+        "author",
+        "maintainer"
+      ],
+      "info" : {
+        "links" : {
+          "email" : "dorien@data-intuitive.com",
+          "github" : "dorien-er",
+          "linkedin" : "dorien-roosen"
+        },
+        "organizations" : [
+          {
+            "name" : "Data Intuitive",
+            "href" : "https://www.data-intuitive.com",
+            "role" : "Data Scientist"
+          }
+        ]
+      }
+    }
+  ],
  "argument_groups" : [
    {
      "name" : "Input",
@@ -2855,46 +2907,50 @@ meta = [
          "name" : "--include_modules",
          "description" : "Use only these module",
          "example" : [
-            "fastqc,cutadapt"
+            "fastqc",
+            "cutadapt"
          ],
          "required" : false,
          "direction" : "input",
          "multiple" : true,
-          "multiple_sep" : ","
+          "multiple_sep" : ";"
        },
        {
          "type" : "string",
          "name" : "--exclude_modules",
          "description" : "Do not use only these modules",
          "example" : [
-            "fastqc,cutadapt"
+            "fastqc",
+            "cutadapt"
          ],
          "required" : false,
          "direction" : "input",
          "multiple" : true,
-          "multiple_sep" : ","
+          "multiple_sep" : ";"
        },
        {
          "type" : "string",
          "name" : "--ignore_analysis",
          "example" : [
-            "run_one/*,run_two/*"
+            "run_one/*",
+            "run_two/*"
          ],
          "required" : false,
          "direction" : "input",
          "multiple" : true,
-          "multiple_sep" : ","
+          "multiple_sep" : ";"
        },
        {
          "type" : "string",
          "name" : "--ignore_samples",
          "example" : [
-            "sample_1*,sample_3*"
+            "sample_1*",
+            "sample_3*"
          ],
          "required" : false,
          "direction" : "input",
          "multiple" : true,
-          "multiple_sep" : ","
+          "multiple_sep" : ";"
        },
        {
          "type" : "boolean_true",
@@ -3279,7 +3335,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3309,22 +3365,22 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/multiqc",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "b84b29747d0635f2ac83ea63b496be9a9edb6724",
+    "viash_version" : "0.9.0",
+    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
    "git_remote" : "https://github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "v0.1.0",
+    "version" : "0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := '0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3411,26 +3467,32 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
 #!/bin/bash

 # disable flags
-[[ "\\$par_ignore_symlinks" == "false" ]] && unset par_ignore_symlinks
-[[ "\\$par_dirs" == "false" ]] && unset par_dirs
-[[ "\\$par_full_names" == "false" ]] && unset par_full_names
-[[ "\\$par_fn_as_s_name" == "false" ]] && unset par_fn_as_s_name
-[[ "\\$par_profile_runtime" == "false" ]] && unset par_profile_runtime
-[[ "\\$par_verbose" == "false" ]] && unset par_verbose
-[[ "\\$par_quiet" == "false" ]] && unset par_quiet
-[[ "\\$par_strict" == "false" ]] && unset par_strict
-[[ "\\$par_development" == "false" ]] && unset par_development
-[[ "\\$par_require_logs" == "false" ]] && unset par_require_logs
-[[ "\\$par_no_megaqc_upload" == "false" ]] && unset par_no_megaqc_upload
-[[ "\\$par_no_ansi" == "false" ]] && unset par_no_ansi
-[[ "\\$par_flat" == "false" ]] && unset par_flat
-[[ "\\$par_interactive" == "false" ]] && unset par_interactive
-[[ "\\$par_static_plot_export" == "false" ]] && unset par_static_plot_export
-[[ "\\$par_data_dir" == "false" ]] && unset par_data_dir
-[[ "\\$par_no_data_dir" == "false" ]] && unset par_no_data_dir
-[[ "\\$par_zip_data_dir" == "false" ]] && unset par_zip_data_dir
-[[ "\\$par_pdf" == "false" ]] && unset par_pdf
+unset_if_false=(
+    par_ignore_symlinks
+    par_dirs
+    par_full_names
+    par_fn_as_s_name
+    par_profile_runtime
+    par_verbose
+    par_quiet
+    par_strict
+    par_development
+    par_require_logs
+    par_no_megaqc_upload
+    par_no_ansi
+    par_flat
+    par_interactive
+    par_static_plot_export
+    par_data_dir
+    par_no_data_dir
+    par_zip_data_dir
+    par_pdf
+)

+for par in \\${unset_if_false[@]}; do
+    test_val="\\${!par}"
+    [[ "\\$test_val" == "false" ]] && unset \\$par
+done

 # handle inputs
 out_dir=\\$(dirname "\\$par_output_report")
@@ -3448,7 +3510,7 @@ IFS=";" read -ra inputs <<< \\$par_input

 if [[ -n "\\$par_include_modules" ]]; then
    include_modules=""
-    IFS="," read -ra incl_modules <<< \\$par_include_modules
+    IFS=";" read -ra incl_modules <<< \\$par_include_modules
    for i in "\\${incl_modules[@]}"; do
        include_modules+="--include \\$i "
    done
@@ -3457,7 +3519,7 @@ fi

 if [[ -n "\\$par_exclude_modules" ]]; then
    exclude_modules=""
-    IFS="," read -ra excl_modules <<< \\$par_exclude_modules
+    IFS=";" read -ra excl_modules <<< \\$par_exclude_modules
    for i in "\\${excl_modules[@]}"; do
        exclude_modules+="--exclude \\$i"
    done
@@ -3466,7 +3528,7 @@ fi

 if [[ -n "\\$par_ignore_analysis" ]]; then
    ignore=""
-    IFS="," read -ra ignore_analysis <<< \\$par_ignore_analysis
+    IFS=";" read -ra ignore_analysis <<< \\$par_ignore_analysis
    for i in "\\${ignore_analysis[@]}"; do
        ignore+="--ignore \\$i "
    done
@@ -3475,7 +3537,7 @@ fi

 if [[ -n "\\$par_ignore_samples" ]]; then
    ignore_samples=""
-    IFS="," read -ra ign_samples <<< \\$par_ignore_samples
+    IFS=";" read -ra ign_samples <<< \\$par_ignore_samples
    for i in "\\${ign_samples[@]}"; do
        ignore_samples+="--ignore-samples \\$i"
    done
@@ -3618,7 +3680,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
              val = val.join(par.multiple_sep)
            }
            if (par.direction == "output" && par.type == "file") {
-              val = val.replaceAll('\\$id', id).replaceAll('\\$key', key)
+              val = val
+                .replaceAll('\\$id', id)
+                .replaceAll('\\$\\{id\\}', id)
+                .replaceAll('\\$key', key)
+                .replaceAll('\\$\\{key\\}', key)
            }
            [parName, val]
          }
@@ -3749,7 +3815,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def createParentStr = meta.config.allArguments
    .findAll { it.type == "file" && it.direction == "output" && it.create_parent }
    .collect { par -> 
-      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
+      def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]"
+      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }"
    }
    .join("\n")

@@ -3757,8 +3824,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def inputFileExports = meta.config.allArguments
    .findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
    .collect { par ->
-      def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
-      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
+      def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}"
+      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}"
    }

  // NOTE: if using docker, use /tmp instead of tmpDir!
@@ -3795,6 +3862,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def procStr = 
  """nextflow.enable.dsl=2
  |
+  |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") }
  |process $procKey {$drctvStrs
  |input:
  |  tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3806,10 +3874,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  |$stub
  |\"\"\"
  |script:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
  |def parInject = args
  |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
  |  .join("\\n")
  |\"\"\"
  |# meta exports
@@ -3894,7 +3961,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/multiqc",
-    "tag" : "v0.1.0"
+    "tag" : "0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow.config
@@ -2,8 +2,9 @@ manifest {
  name = 'multiqc'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = '0.2.0'
  description = 'MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n'
+  author = 'Dorien Roosen'
 }

 process.container = 'nextflow/bash:latest'
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow_schema.json
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow_schema.json
@@ -17,8 +17,8 @@
                "input": {
                "type":
                "string",
-                "description": "Type: List of `file`, required, example: `data/results/`, multiple_sep: `\":\"`. File paths to be searched for analysis results to be included in the report",
-                "help_text": "Type: List of `file`, required, example: `data/results/`, multiple_sep: `\":\"`. File paths to be searched for analysis results to be included in the report.\n"
+                "description": "Type: List of `file`, required, example: `data/results`, multiple_sep: `\";\"`. File paths to be searched for analysis results to be included in the report",
+                "help_text": "Type: List of `file`, required, example: `data/results`, multiple_sep: `\";\"`. File paths to be searched for analysis results to be included in the report.\n"
            
            }
    
@@ -80,8 +80,8 @@
                "include_modules": {
                "type":
                "string",
-                "description": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Use only these module",
-                "help_text": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Use only these module"
+                "description": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Use only these module",
+                "help_text": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Use only these module"
            
            }
    
@@ -90,8 +90,8 @@
                "exclude_modules": {
                "type":
                "string",
-                "description": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Do not use only these modules",
-                "help_text": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Do not use only these modules"
+                "description": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Do not use only these modules",
+                "help_text": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Do not use only these modules"
            
            }
    
@@ -100,8 +100,8 @@
                "ignore_analysis": {
                "type":
                "string",
-                "description": "Type: List of `string`, example: `run_one/*,run_two/*`, multiple_sep: `\",\"`. ",
-                "help_text": "Type: List of `string`, example: `run_one/*,run_two/*`, multiple_sep: `\",\"`. "
+                "description": "Type: List of `string`, example: `run_one/*;run_two/*`, multiple_sep: `\";\"`. ",
+                "help_text": "Type: List of `string`, example: `run_one/*;run_two/*`, multiple_sep: `\";\"`. "
            
            }
    
@@ -110,8 +110,8 @@
                "ignore_samples": {
                "type":
                "string",
-                "description": "Type: List of `string`, example: `sample_1*,sample_3*`, multiple_sep: `\",\"`. ",
-                "help_text": "Type: List of `string`, example: `sample_1*,sample_3*`, multiple_sep: `\",\"`. "
+                "description": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. ",
+                "help_text": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. "
            
            }
    
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -116,7 +116,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -140,25 +140,25 @@ build_info:
  engine: "docker|native"
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
-  viash_version: "0.9.0-RC6"
-  git_commit: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "5ad947dd1e6d6783ac7905d665036733a420731f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -1,10 +1,10 @@
 #!/usr/bin/env bash

-# interop_summary_to_csv v0.1.0
+# interop_summary_to_csv v0.1.1
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+# Intuitive.
 # 
 # The component may contain files which fall under a different license. The
 # authors of this component should specify the license in the header of such
@@ -54,24 +54,24 @@ function ViashRemoveFlags {
 # $1      : Should always be set to ${BASH_SOURCE[0]}
 # returns : The absolute path of the bash file
 function ViashSourceDir {
-  SOURCE="$1"
-  while [ -h "$SOURCE" ]; do
-    DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-    SOURCE="$(readlink "$SOURCE")"
-    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+  local source="$1"
+  while [ -h "$source" ]; do
+    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
+    source="$(readlink "$source")"
+    [[ $source != /* ]] && source="$dir/$source"
  done
-  cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd
+  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
 }
 # ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
 # usage   : ViashFindTargetDir 'ScriptPath'
 # $1      : The location from where to start the upward search
 # returns : The absolute path of the '.build.yaml' file
 function ViashFindTargetDir {
-  SOURCE="$1"
-  while [[ "$SOURCE" != "" && ! -e "$SOURCE/.build.yaml" ]]; do
-    SOURCE=${SOURCE%/*}
+  local source="$1"
+  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
+    source=${source%/*}
  done
-  echo $SOURCE
+  echo $source
 }
 # see https://en.wikipedia.org/wiki/Syslog#Severity_level
 VIASH_LOGCODE_EMERGENCY=0
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "interop_summary_to_csv v0.1.0"
+  echo "interop_summary_to_csv v0.1.1"
  echo ""
  echo "Input arguments:"
  echo "    --input"
@@ -205,9 +205,9 @@ function ViashDockerInstallationCheck {
  fi

  ViashDebug "Checking whether the Docker daemon is running"
-  save=$-; set +e
-  docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  out=$?
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
@@ -259,9 +259,9 @@ function ViashDockerPull {
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker pull $1 && return 0 || return 1
  else
-    save=$-; set +e
+    local save=$-; set +e
    docker pull $1 2> /dev/null > /dev/null
-    out=$?
+    local out=$?
    [[ $save =~ e ]] && set -e
    if [ $out -ne 0 ]; then
      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
@@ -281,7 +281,8 @@ function ViashDockerPull {
 #   echo $?                                     # returns '1'
 function ViashDockerPush {
  ViashNotice "Pushing image to '$1'"
-  save=$-; set +e
+  local save=$-; set +e
+  local out
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker push $1
    out=$?
@@ -305,9 +306,9 @@ function ViashDockerPush {
 # examples:
 #   ViashDockerPullElseBuild mynewcomponent
 function ViashDockerPullElseBuild {
-  save=$-; set +e
+  local save=$-; set +e
  ViashDockerPull $1
-  out=$?
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashDockerBuild $@
@@ -469,10 +470,10 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
 mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
-LABEL org.opencontainers.image.created="2024-06-24T12:57:03Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:00:09Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="3d229bef584233f228330ff881dad685b92bf1e1"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="5ad947dd1e6d6783ac7905d665036733a420731f"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -498,6 +499,9 @@ function ViashDockerBuildArgs {
 #   ViashAbsolutePath /foo/bar/..     # returns /foo
 function ViashAbsolutePath {
  local thePath
+  local parr
+  local outp
+  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
@@ -528,14 +532,17 @@ function ViashAbsolutePath {
  )
 }
 # ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                  : The parameter value
-# returns             : New parameter
-# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
 # examples:
 #   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
 #   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
 function ViashDockerAutodetectMount {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -543,7 +550,7 @@ function ViashDockerAutodetectMount {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  if [ -z "$base_name" ]; then
    echo "$mount_target"
  else
@@ -551,7 +558,9 @@ function ViashDockerAutodetectMount {
  fi
 }
 function ViashDockerAutodetectMountArg {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -559,17 +568,22 @@ function ViashDockerAutodetectMountArg {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
  echo "--volume=\"$mount_source:$mount_target\""
 }
 function ViashDockerStripAutomount {
-  abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#/viash_automount}"
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
 }
 # initialise variables
 VIASH_DIRECTORY_MOUNTS=()

+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)

@@ -595,7 +609,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "interop_summary_to_csv v0.1.0"
+            echo "interop_summary_to_csv v0.1.1"
            exit
            ;;
        --input)
@@ -653,6 +667,18 @@ while [[ $# -gt 0 ]]; do
            VIASH_MODE='dockerfile'
            shift 1
            ;;
+        ---docker_run_args)
+            VIASH_DOCKER_RUN_ARGS+=("$2")
+            shift 2
+            ;;
+        ---docker_run_args=*)
+            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
@@ -707,13 +733,17 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.1.1'
  fi

  # print dockerfile
  if [ "$VIASH_MODE" == "dockerfile" ]; then
    ViashDockerfile "$VIASH_ENGINE_ID"
    exit 0
+
+  elif [ "$VIASH_MODE" == "docker_image_id" ]; then
+    echo "$VIASH_DOCKER_IMAGE_ID"
+    exit 0
  
  # enter docker container
  elif [[ "$VIASH_MODE" == "debug" ]]; then
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -130,7 +130,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -147,25 +147,25 @@ build_info:
  engine: "docker|native"
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
-  viash_version: "0.9.0-RC6"
-  git_commit: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "5ad947dd1e6d6783ac7905d665036733a420731f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -1,10 +1,10 @@
 #!/usr/bin/env bash

-# untar v0.1.0
+# untar v0.1.1
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-# Data Intuitive.
+# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+# Intuitive.
 # 
 # The component may contain files which fall under a different license. The
 # authors of this component should specify the license in the header of such
@@ -54,24 +54,24 @@ function ViashRemoveFlags {
 # $1      : Should always be set to ${BASH_SOURCE[0]}
 # returns : The absolute path of the bash file
 function ViashSourceDir {
-  SOURCE="$1"
-  while [ -h "$SOURCE" ]; do
-    DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-    SOURCE="$(readlink "$SOURCE")"
-    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+  local source="$1"
+  while [ -h "$source" ]; do
+    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
+    source="$(readlink "$source")"
+    [[ $source != /* ]] && source="$dir/$source"
  done
-  cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd
+  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
 }
 # ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
 # usage   : ViashFindTargetDir 'ScriptPath'
 # $1      : The location from where to start the upward search
 # returns : The absolute path of the '.build.yaml' file
 function ViashFindTargetDir {
-  SOURCE="$1"
-  while [[ "$SOURCE" != "" && ! -e "$SOURCE/.build.yaml" ]]; do
-    SOURCE=${SOURCE%/*}
+  local source="$1"
+  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
+    source=${source%/*}
  done
-  echo $SOURCE
+  echo $source
 }
 # see https://en.wikipedia.org/wiki/Syslog#Severity_level
 VIASH_LOGCODE_EMERGENCY=0
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.1.0"
+  echo "untar v0.1.1"
  echo ""
  echo "Unpack a .tar file. When the contents of the .tar file is just a single"
  echo "directory,"
@@ -215,9 +215,9 @@ function ViashDockerInstallationCheck {
  fi

  ViashDebug "Checking whether the Docker daemon is running"
-  save=$-; set +e
-  docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  out=$?
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
@@ -269,9 +269,9 @@ function ViashDockerPull {
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker pull $1 && return 0 || return 1
  else
-    save=$-; set +e
+    local save=$-; set +e
    docker pull $1 2> /dev/null > /dev/null
-    out=$?
+    local out=$?
    [[ $save =~ e ]] && set -e
    if [ $out -ne 0 ]; then
      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
@@ -291,7 +291,8 @@ function ViashDockerPull {
 #   echo $?                                     # returns '1'
 function ViashDockerPush {
  ViashNotice "Pushing image to '$1'"
-  save=$-; set +e
+  local save=$-; set +e
+  local out
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker push $1
    out=$?
@@ -315,9 +316,9 @@ function ViashDockerPush {
 # examples:
 #   ViashDockerPullElseBuild mynewcomponent
 function ViashDockerPullElseBuild {
-  save=$-; set +e
+  local save=$-; set +e
  ViashDockerPull $1
-  out=$?
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashDockerBuild $@
@@ -475,10 +476,10 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io untar"
-LABEL org.opencontainers.image.created="2024-06-24T12:57:03Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:00:08Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="3d229bef584233f228330ff881dad685b92bf1e1"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="5ad947dd1e6d6783ac7905d665036733a420731f"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -504,6 +505,9 @@ function ViashDockerBuildArgs {
 #   ViashAbsolutePath /foo/bar/..     # returns /foo
 function ViashAbsolutePath {
  local thePath
+  local parr
+  local outp
+  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
@@ -534,14 +538,17 @@ function ViashAbsolutePath {
  )
 }
 # ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                  : The parameter value
-# returns             : New parameter
-# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
 # examples:
 #   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
 #   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
 function ViashDockerAutodetectMount {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -549,7 +556,7 @@ function ViashDockerAutodetectMount {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  if [ -z "$base_name" ]; then
    echo "$mount_target"
  else
@@ -557,7 +564,9 @@ function ViashDockerAutodetectMount {
  fi
 }
 function ViashDockerAutodetectMountArg {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -565,17 +574,22 @@ function ViashDockerAutodetectMountArg {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
  echo "--volume=\"$mount_source:$mount_target\""
 }
 function ViashDockerStripAutomount {
-  abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#/viash_automount}"
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
 }
 # initialise variables
 VIASH_DIRECTORY_MOUNTS=()

+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)

@@ -601,7 +615,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "untar v0.1.0"
+            echo "untar v0.1.1"
            exit
            ;;
        --input)
@@ -665,6 +679,18 @@ while [[ $# -gt 0 ]]; do
            VIASH_MODE='dockerfile'
            shift 1
            ;;
+        ---docker_run_args)
+            VIASH_DOCKER_RUN_ARGS+=("$2")
+            shift 2
+            ;;
+        ---docker_run_args=*)
+            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
@@ -719,13 +745,17 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.1.1'
  fi

  # print dockerfile
  if [ "$VIASH_MODE" == "dockerfile" ]; then
    ViashDockerfile "$VIASH_ENGINE_ID"
    exit 0
+
+  elif [ "$VIASH_MODE" == "docker_image_id" ]; then
+    echo "$VIASH_DOCKER_IMAGE_ID"
+    exit 0
  
  # enter docker container
  elif [[ "$VIASH_MODE" == "debug" ]]; then
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "combine_samples"
 namespace: "dataflow"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -138,25 +138,25 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "5ad947dd1e6d6783ac7905d665036733a420731f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,8 +1,8 @@
-// combine_samples v0.1.0
+// combine_samples v0.1.1
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
@@ -760,8 +760,11 @@ def runEach(Map args) {
  def fromState_ = args.fromState
  def toState_ = args.toState
  def filter_ = args.filter
+  def runIf_ = args.runIf
  def id_ = args.id

+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
  workflow runEachWf {
    take: input_ch
    main:
@@ -783,7 +786,20 @@ def runEach(Map args) {
          [new_id] + tup.drop(1)
        }
        : filter_ch
-      def data_ch = id_ch | map{tup ->
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
          def new_data = tup[1]
          if (fromState_ instanceof Map) {
            new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +837,11 @@ def runEach(Map args) {
          [tup[0], new_state] + tup.drop(3)
        }
        : out_ch
+
+      def return_ch = post_ch
+        | concat(chPassthrough)
      
-      post_ch
+      return_ch
    }

    // mix all results
@@ -1598,8 +1617,8 @@ def findStates(Map params, Map config) {
          // construct renameMap
          if (args.rename_keys) {
            def renameMap = args.rename_keys.collectEntries{renameString ->
-              def split = renameString.split(";")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
              split
            }

@@ -1709,7 +1728,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1801,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .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
@@ -1822,7 +1845,9 @@ def publishStatesByConfig(Map args) {
                // 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
@@ -2626,30 +2651,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
        tuple
      }

-    def chModifiedFiltered = workflowArgs.filter ?
-      chModified | filter{workflowArgs.filter(it)} :
-      chModified

    def chRun = null
    def chPassthrough = null
    if (workflowArgs.runIf) {
-      def runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModified.branch{ tup ->
        run: workflowArgs.runIf(tup[0], tup[1])
        passthrough: true
      }
      chRun = runIfBranch.run
      chPassthrough = runIfBranch.passthrough
    } else {
-      chRun = chModifiedFiltered
+      chRun = chModified
      chPassthrough = Channel.empty()
    }

+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
    def chArgs = workflowArgs.fromState ? 
-      chRun | map{
+      chRunFiltered | map{
        def new_data = workflowArgs.fromState(it.take(2))
        [it[0], new_data]
      } :
-      chRun | map {tup -> tup.take(2)}
+      chRunFiltered | map {tup -> tup.take(2)}

    // fill in defaults
    def chArgsWithDefaults = chArgs
@@ -2720,7 +2746,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
      // | view{"chInitialOutput: ${it.take(3)}"}

    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
      // input tuple format: [join_id, id, output, prev_state, ...]
      // output tuple format: [join_id, id, new_state, ...]
      | map{ tup ->
@@ -2780,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "combine_samples",
  "namespace" : "dataflow",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2945,13 +2971,13 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "3d229bef584233f228330ff881dad685b92bf1e1",
+    "viash_version" : "0.9.0",
+    "git_commit" : "5ad947dd1e6d6783ac7905d665036733a420731f",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -2961,14 +2987,14 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/dataflow/combine_samples/nextflow.config
+++ b/target/nextflow/dataflow/combine_samples/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'dataflow/combine_samples'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
  description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
 }

--- a/target/nextflow/dataflow/combine_samples/nextflow_schema.json
+++ b/target/nextflow/dataflow/combine_samples/nextflow_schema.json
@@ -57,8 +57,8 @@
                "output_forward": {
                "type":
                "string",
-                "description": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\":\"`. ",
-                "help_text": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\":\"`. "
+                "description": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\";\"`. ",
+                "help_text": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\";\"`. "
            ,
                "default": "$id.$key.output_forward_*.output_forward_*"
            }
@@ -68,8 +68,8 @@
                "output_reverse": {
                "type":
                "string",
-                "description": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\":\"`. ",
-                "help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\":\"`. "
+                "description": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\";\"`. ",
+                "help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\";\"`. "
            ,
                "default": "$id.$key.output_reverse_*.output_reverse_*"
            }
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "gather_fastqs_and_validate"
 namespace: "dataflow"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -132,25 +132,25 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/dataflow/gather_fastqs_and_validate"
  executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "5ad947dd1e6d6783ac7905d665036733a420731f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -1,8 +1,8 @@
-// gather_fastqs_and_validate v0.1.0
+// gather_fastqs_and_validate v0.1.1
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
@@ -760,8 +760,11 @@ def runEach(Map args) {
  def fromState_ = args.fromState
  def toState_ = args.toState
  def filter_ = args.filter
+  def runIf_ = args.runIf
  def id_ = args.id

+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
  workflow runEachWf {
    take: input_ch
    main:
@@ -783,7 +786,20 @@ def runEach(Map args) {
          [new_id] + tup.drop(1)
        }
        : filter_ch
-      def data_ch = id_ch | map{tup ->
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
          def new_data = tup[1]
          if (fromState_ instanceof Map) {
            new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +837,11 @@ def runEach(Map args) {
          [tup[0], new_state] + tup.drop(3)
        }
        : out_ch
+
+      def return_ch = post_ch
+        | concat(chPassthrough)
      
-      post_ch
+      return_ch
    }

    // mix all results
@@ -1598,8 +1617,8 @@ def findStates(Map params, Map config) {
          // construct renameMap
          if (args.rename_keys) {
            def renameMap = args.rename_keys.collectEntries{renameString ->
-              def split = renameString.split(";")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
              split
            }

@@ -1709,7 +1728,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1801,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .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
@@ -1822,7 +1845,9 @@ def publishStatesByConfig(Map args) {
                // 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
@@ -2626,30 +2651,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
        tuple
      }

-    def chModifiedFiltered = workflowArgs.filter ?
-      chModified | filter{workflowArgs.filter(it)} :
-      chModified

    def chRun = null
    def chPassthrough = null
    if (workflowArgs.runIf) {
-      def runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModified.branch{ tup ->
        run: workflowArgs.runIf(tup[0], tup[1])
        passthrough: true
      }
      chRun = runIfBranch.run
      chPassthrough = runIfBranch.passthrough
    } else {
-      chRun = chModifiedFiltered
+      chRun = chModified
      chPassthrough = Channel.empty()
    }

+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
    def chArgs = workflowArgs.fromState ? 
-      chRun | map{
+      chRunFiltered | map{
        def new_data = workflowArgs.fromState(it.take(2))
        [it[0], new_data]
      } :
-      chRun | map {tup -> tup.take(2)}
+      chRunFiltered | map {tup -> tup.take(2)}

    // fill in defaults
    def chArgsWithDefaults = chArgs
@@ -2720,7 +2746,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
      // | view{"chInitialOutput: ${it.take(3)}"}

    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
      // input tuple format: [join_id, id, output, prev_state, ...]
      // output tuple format: [join_id, id, new_state, ...]
      | map{ tup ->
@@ -2780,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "gather_fastqs_and_validate",
  "namespace" : "dataflow",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2938,13 +2964,13 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "3d229bef584233f228330ff881dad685b92bf1e1",
+    "viash_version" : "0.9.0",
+    "git_commit" : "5ad947dd1e6d6783ac7905d665036733a420731f",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -2954,14 +2980,14 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
    ],
    "keywords" : [
      "bioinformatics",
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'dataflow/gather_fastqs_and_validate'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
  description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
 }

--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "demultiplex"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -93,22 +93,22 @@ dependencies:
  repository:
    type: "vsh"
    repo: "biobox"
-    tag: "v0.1.0"
+    tag: "v0.2.0"
 - name: "falco"
  repository:
    type: "vsh"
    repo: "biobox"
-    tag: "v0.1.0"
+    tag: "v0.2.0"
 - name: "multiqc"
  repository:
    type: "vsh"
    repo: "biobox"
-    tag: "v0.1.0"
+    tag: "v0.2.0"
 repositories:
 - type: "vsh"
  name: "bb"
  repo: "biobox"
-  tag: "v0.1.0"
+  tag: "v0.2.0"
 license: "MIT"
 links:
  repository: "https://github.com/viash-hub/demultiplex"
@@ -185,33 +185,33 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "5ad947dd1e6d6783ac7905d665036733a420731f"
  git_remote: "https://github.com/viash-hub/demultiplex"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
  - "target/nextflow/io/interop_summary_to_csv"
  - "target/nextflow/dataflow/combine_samples"
-  - "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert"
-  - "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco"
-  - "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc"
 package_config:
  name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -1,8 +1,8 @@
-// demultiplex v0.1.0
+// demultiplex v0.1.1
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
@@ -760,8 +760,11 @@ def runEach(Map args) {
  def fromState_ = args.fromState
  def toState_ = args.toState
  def filter_ = args.filter
+  def runIf_ = args.runIf
  def id_ = args.id

+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
  workflow runEachWf {
    take: input_ch
    main:
@@ -783,7 +786,20 @@ def runEach(Map args) {
          [new_id] + tup.drop(1)
        }
        : filter_ch
-      def data_ch = id_ch | map{tup ->
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
          def new_data = tup[1]
          if (fromState_ instanceof Map) {
            new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +837,11 @@ def runEach(Map args) {
          [tup[0], new_state] + tup.drop(3)
        }
        : out_ch
+
+      def return_ch = post_ch
+        | concat(chPassthrough)
      
-      post_ch
+      return_ch
    }

    // mix all results
@@ -1598,8 +1617,8 @@ def findStates(Map params, Map config) {
          // construct renameMap
          if (args.rename_keys) {
            def renameMap = args.rename_keys.collectEntries{renameString ->
-              def split = renameString.split(";")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
              split
            }

@@ -1709,7 +1728,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1801,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .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
@@ -1822,7 +1845,9 @@ def publishStatesByConfig(Map args) {
                // 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
@@ -2626,30 +2651,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
        tuple
      }

-    def chModifiedFiltered = workflowArgs.filter ?
-      chModified | filter{workflowArgs.filter(it)} :
-      chModified

    def chRun = null
    def chPassthrough = null
    if (workflowArgs.runIf) {
-      def runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModified.branch{ tup ->
        run: workflowArgs.runIf(tup[0], tup[1])
        passthrough: true
      }
      chRun = runIfBranch.run
      chPassthrough = runIfBranch.passthrough
    } else {
-      chRun = chModifiedFiltered
+      chRun = chModified
      chPassthrough = Channel.empty()
    }

+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
    def chArgs = workflowArgs.fromState ? 
-      chRun | map{
+      chRunFiltered | map{
        def new_data = workflowArgs.fromState(it.take(2))
        [it[0], new_data]
      } :
-      chRun | map {tup -> tup.take(2)}
+      chRunFiltered | map {tup -> tup.take(2)}

    // fill in defaults
    def chArgsWithDefaults = chArgs
@@ -2720,7 +2746,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
      // | view{"chInitialOutput: ${it.take(3)}"}

    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
      // input tuple format: [join_id, id, output, prev_state, ...]
      // output tuple format: [join_id, id, new_state, ...]
      | map{ tup ->
@@ -2779,7 +2805,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "demultiplex",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2906,7 +2932,7 @@ meta = [
      "repository" : {
        "type" : "vsh",
        "repo" : "biobox",
-        "tag" : "v0.1.0"
+        "tag" : "v0.2.0"
      }
    },
    {
@@ -2914,7 +2940,7 @@ meta = [
      "repository" : {
        "type" : "vsh",
        "repo" : "biobox",
-        "tag" : "v0.1.0"
+        "tag" : "v0.2.0"
      }
    },
    {
@@ -2922,7 +2948,7 @@ meta = [
      "repository" : {
        "type" : "vsh",
        "repo" : "biobox",
-        "tag" : "v0.1.0"
+        "tag" : "v0.2.0"
      }
    }
  ],
@@ -2931,7 +2957,7 @@ meta = [
      "type" : "vsh",
      "name" : "bb",
      "repo" : "biobox",
-      "tag" : "v0.1.0"
+      "tag" : "v0.2.0"
    }
  ],
  "license" : "MIT",
@@ -3022,13 +3048,13 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "3d229bef584233f228330ff881dad685b92bf1e1",
+    "viash_version" : "0.9.0",
+    "git_commit" : "5ad947dd1e6d6783ac7905d665036733a420731f",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -3038,14 +3064,14 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3069,9 +3095,9 @@ include { untar } from "${meta.resources_dir}/../../nextflow/io/untar/main.nf"
 include { gather_fastqs_and_validate } from "${meta.resources_dir}/../../nextflow/dataflow/gather_fastqs_and_validate/main.nf"
 include { interop_summary_to_csv } from "${meta.resources_dir}/../../nextflow/io/interop_summary_to_csv/main.nf"
 include { combine_samples } from "${meta.resources_dir}/../../nextflow/dataflow/combine_samples/main.nf"
-include { bcl_convert } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/main.nf"
-include { falco } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/main.nf"
-include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/main.nf"
+include { bcl_convert } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/main.nf"
+include { falco } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/main.nf"
+include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf"

 // inner workflow
 // user-provided Nextflow code
--- a/target/nextflow/demultiplex/nextflow.config
+++ b/target/nextflow/demultiplex/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'demultiplex'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
  description = 'Demultiplexing of raw sequencing data'
 }

--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "interop_summary_to_csv"
 namespace: "io"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -116,7 +116,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -140,25 +140,25 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/io/interop_summary_to_csv"
  executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "5ad947dd1e6d6783ac7905d665036733a420731f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -1,8 +1,8 @@
-// interop_summary_to_csv v0.1.0
+// interop_summary_to_csv v0.1.1
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
@@ -760,8 +760,11 @@ def runEach(Map args) {
  def fromState_ = args.fromState
  def toState_ = args.toState
  def filter_ = args.filter
+  def runIf_ = args.runIf
  def id_ = args.id

+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
  workflow runEachWf {
    take: input_ch
    main:
@@ -783,7 +786,20 @@ def runEach(Map args) {
          [new_id] + tup.drop(1)
        }
        : filter_ch
-      def data_ch = id_ch | map{tup ->
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
          def new_data = tup[1]
          if (fromState_ instanceof Map) {
            new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +837,11 @@ def runEach(Map args) {
          [tup[0], new_state] + tup.drop(3)
        }
        : out_ch
+
+      def return_ch = post_ch
+        | concat(chPassthrough)
      
-      post_ch
+      return_ch
    }

    // mix all results
@@ -1598,8 +1617,8 @@ def findStates(Map params, Map config) {
          // construct renameMap
          if (args.rename_keys) {
            def renameMap = args.rename_keys.collectEntries{renameString ->
-              def split = renameString.split(";")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
              split
            }

@@ -1709,7 +1728,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1801,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .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
@@ -1822,7 +1845,9 @@ def publishStatesByConfig(Map args) {
                // 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
@@ -2626,30 +2651,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
        tuple
      }

-    def chModifiedFiltered = workflowArgs.filter ?
-      chModified | filter{workflowArgs.filter(it)} :
-      chModified

    def chRun = null
    def chPassthrough = null
    if (workflowArgs.runIf) {
-      def runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModified.branch{ tup ->
        run: workflowArgs.runIf(tup[0], tup[1])
        passthrough: true
      }
      chRun = runIfBranch.run
      chPassthrough = runIfBranch.passthrough
    } else {
-      chRun = chModifiedFiltered
+      chRun = chModified
      chPassthrough = Channel.empty()
    }

+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
    def chArgs = workflowArgs.fromState ? 
-      chRun | map{
+      chRunFiltered | map{
        def new_data = workflowArgs.fromState(it.take(2))
        [it[0], new_data]
      } :
-      chRun | map {tup -> tup.take(2)}
+      chRunFiltered | map {tup -> tup.take(2)}

    // fill in defaults
    def chArgsWithDefaults = chArgs
@@ -2720,7 +2746,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
      // | view{"chInitialOutput: ${it.take(3)}"}

    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
      // input tuple format: [join_id, id, output, prev_state, ...]
      // output tuple format: [join_id, id, new_state, ...]
      | map{ tup ->
@@ -2780,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "interop_summary_to_csv",
  "namespace" : "io",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2921,7 +2947,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -2950,13 +2976,13 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "3d229bef584233f228330ff881dad685b92bf1e1",
+    "viash_version" : "0.9.0",
+    "git_commit" : "5ad947dd1e6d6783ac7905d665036733a420731f",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -2966,14 +2992,14 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3115,7 +3141,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
              val = val.join(par.multiple_sep)
            }
            if (par.direction == "output" && par.type == "file") {
-              val = val.replaceAll('\\$id', id).replaceAll('\\$key', key)
+              val = val
+                .replaceAll('\\$id', id)
+                .replaceAll('\\$\\{id\\}', id)
+                .replaceAll('\\$key', key)
+                .replaceAll('\\$\\{key\\}', key)
            }
            [parName, val]
          }
@@ -3246,7 +3276,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def createParentStr = meta.config.allArguments
    .findAll { it.type == "file" && it.direction == "output" && it.create_parent }
    .collect { par -> 
-      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
+      def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]"
+      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }"
    }
    .join("\n")

@@ -3254,8 +3285,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def inputFileExports = meta.config.allArguments
    .findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
    .collect { par ->
-      def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
-      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
+      def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}"
+      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}"
    }

  // NOTE: if using docker, use /tmp instead of tmpDir!
@@ -3292,6 +3323,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def procStr = 
  """nextflow.enable.dsl=2
  |
+  |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") }
  |process $procKey {$drctvStrs
  |input:
  |  tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3303,10 +3335,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  |$stub
  |\"\"\"
  |script:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
  |def parInject = args
  |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
  |  .join("\\n")
  |\"\"\"
  |# meta exports
@@ -3391,7 +3422,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/interop_summary_to_csv",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/interop_summary_to_csv/nextflow.config
+++ b/target/nextflow/io/interop_summary_to_csv/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/interop_summary_to_csv'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
 }

 process.container = 'nextflow/bash:latest'
--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "untar"
 namespace: "io"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -130,7 +130,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -147,25 +147,25 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
-  viash_version: "0.9.0-RC6"
-  git_commit: "3d229bef584233f228330ff881dad685b92bf1e1"
+  viash_version: "0.9.0"
+  git_commit: "5ad947dd1e6d6783ac7905d665036733a420731f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
-  version: "v0.1.0"
+  version: "v0.1.1"
  description: "Demultiplexing pipeline\n"
  info:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  keywords:
  - "bioinformatics"
  - "sequence"
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -1,8 +1,8 @@
-// untar v0.1.0
+// untar v0.1.1
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
-// Data Intuitive.
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
+// Intuitive.
 // 
 // The component may contain files which fall under a different license. The
 // authors of this component should specify the license in the header of such
@@ -760,8 +760,11 @@ def runEach(Map args) {
  def fromState_ = args.fromState
  def toState_ = args.toState
  def filter_ = args.filter
+  def runIf_ = args.runIf
  def id_ = args.id

+  assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
+
  workflow runEachWf {
    take: input_ch
    main:
@@ -783,7 +786,20 @@ def runEach(Map args) {
          [new_id] + tup.drop(1)
        }
        : filter_ch
-      def data_ch = id_ch | map{tup ->
+      def chPassthrough = null
+      def chRun = null
+      if (runIf_) {
+        def idRunIfBranch = id_ch.branch{ tup ->
+          run: runIf_(tup[0], tup[1], comp_)
+          passthrough: true
+        }
+        chPassthrough = idRunIfBranch.passthrough
+        chRun = idRunIfBranch.run
+      } else {
+        chRun = id_ch
+        chPassthrough = Channel.empty()
+      }
+      def data_ch = chRun | map{tup ->
          def new_data = tup[1]
          if (fromState_ instanceof Map) {
            new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +837,11 @@ def runEach(Map args) {
          [tup[0], new_state] + tup.drop(3)
        }
        : out_ch
+
+      def return_ch = post_ch
+        | concat(chPassthrough)
      
-      post_ch
+      return_ch
    }

    // mix all results
@@ -1598,8 +1617,8 @@ def findStates(Map params, Map config) {
          // construct renameMap
          if (args.rename_keys) {
            def renameMap = args.rename_keys.collectEntries{renameString ->
-              def split = renameString.split(";")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
              split
            }

@@ -1709,7 +1728,9 @@ def publishStates(Map args) {

          def yamlFilename = yamlTemplate_
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .replaceAll('\\$\\{key\\}', key_)

            // TODO: do the pathnames in state_ match up with the outputFilenames_?

@@ -1780,7 +1801,9 @@ def publishStatesByConfig(Map args) {
          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
          def yamlFilename = yamlTemplate
            .replaceAll('\\$id', id_)
+            .replaceAll('\\$\\{id\\}', id_)
            .replaceAll('\\$key', key_)
+            .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
@@ -1822,7 +1845,9 @@ def publishStatesByConfig(Map args) {
                // 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
@@ -2626,30 +2651,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
        tuple
      }

-    def chModifiedFiltered = workflowArgs.filter ?
-      chModified | filter{workflowArgs.filter(it)} :
-      chModified

    def chRun = null
    def chPassthrough = null
    if (workflowArgs.runIf) {
-      def runIfBranch = chModifiedFiltered.branch{ tup ->
+      def runIfBranch = chModified.branch{ tup ->
        run: workflowArgs.runIf(tup[0], tup[1])
        passthrough: true
      }
      chRun = runIfBranch.run
      chPassthrough = runIfBranch.passthrough
    } else {
-      chRun = chModifiedFiltered
+      chRun = chModified
      chPassthrough = Channel.empty()
    }

+    def chRunFiltered = workflowArgs.filter ?
+      chRun | filter{workflowArgs.filter(it)} :
+      chRun
+
    def chArgs = workflowArgs.fromState ? 
-      chRun | map{
+      chRunFiltered | map{
        def new_data = workflowArgs.fromState(it.take(2))
        [it[0], new_data]
      } :
-      chRun | map {tup -> tup.take(2)}
+      chRunFiltered | map {tup -> tup.take(2)}

    // fill in defaults
    def chArgsWithDefaults = chArgs
@@ -2720,7 +2746,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
      // | view{"chInitialOutput: ${it.take(3)}"}

    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
      // input tuple format: [join_id, id, output, prev_state, ...]
      // output tuple format: [join_id, id, new_state, ...]
      | map{ tup ->
@@ -2780,7 +2806,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "untar",
  "namespace" : "io",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2940,7 +2966,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -2962,13 +2988,13 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
-    "viash_version" : "0.9.0-RC6",
-    "git_commit" : "3d229bef584233f228330ff881dad685b92bf1e1",
+    "viash_version" : "0.9.0",
+    "git_commit" : "5ad947dd1e6d6783ac7905d665036733a420731f",
    "git_remote" : "https://github.com/viash-hub/demultiplex"
  },
  "package_config" : {
    "name" : "demultiplex",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
    "description" : "Demultiplexing pipeline\n",
    "info" : {
      "test_resources" : [
@@ -2978,14 +3004,14 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.0-RC6",
+    "viash_version" : "0.9.0",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3157,7 +3183,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
              val = val.join(par.multiple_sep)
            }
            if (par.direction == "output" && par.type == "file") {
-              val = val.replaceAll('\\$id', id).replaceAll('\\$key', key)
+              val = val
+                .replaceAll('\\$id', id)
+                .replaceAll('\\$\\{id\\}', id)
+                .replaceAll('\\$key', key)
+                .replaceAll('\\$\\{key\\}', key)
            }
            [parName, val]
          }
@@ -3288,7 +3318,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def createParentStr = meta.config.allArguments
    .findAll { it.type == "file" && it.direction == "output" && it.create_parent }
    .collect { par -> 
-      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
+      def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]"
+      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }"
    }
    .join("\n")

@@ -3296,8 +3327,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def inputFileExports = meta.config.allArguments
    .findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
    .collect { par ->
-      def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
-      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
+      def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}"
+      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}"
    }

  // NOTE: if using docker, use /tmp instead of tmpDir!
@@ -3334,6 +3365,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  def procStr = 
  """nextflow.enable.dsl=2
  |
+  |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") }
  |process $procKey {$drctvStrs
  |input:
  |  tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3345,10 +3377,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  |$stub
  |\"\"\"
  |script:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
  |def parInject = args
  |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
  |  .join("\\n")
  |\"\"\"
  |# meta exports
@@ -3433,7 +3464,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/demultiplex/io/untar",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/io/untar/nextflow.config
+++ b/target/nextflow/io/untar/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'io/untar'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
  description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n'
 }