Build branch main with version main (399e469)

Build pipeline: viash-hub.demultiplex.main-f55jt

Source commit: 399e46901d

Source message: Add test_resources to .gitignore

.gitignore

@@ -1,7 +1,8 @@
 target
 testData
+test_resources
 
 # Nextflow related files
 .nextflow
 .nextflow.log*
-work
+work

CHANGELOG.md

@@ -1,17 +1,13 @@
-# 0.1.2
+# Unreleased
 
-## 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

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

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"
+  viash_version: "0.9.0"
-  git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724"
+  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"

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
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
-// Data Intuitive.
+// 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(";")
+              def split = renameString.split(":")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              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",
+    "viash_version" : "0.9.0",
-    "git_commit" : "b84b29747d0635f2ac83ea63b496be9a9edb6724",
+    "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})"
+      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()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
+      "\n\${viash_par_${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"
 }'''),

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'

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"
+  viash_version: "0.9.0"
-  git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724"
+  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"

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
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
-// Data Intuitive.
+// 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(";")
+              def split = renameString.split(":")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              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",
+    "viash_version" : "0.9.0",
-    "git_commit" : "b84b29747d0635f2ac83ea63b496be9a9edb6724",
+    "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})"
+      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()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
+      "\n\${viash_par_${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"
 }'''),

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'

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",
+                "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"
+                "help_text": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\";\"`. input fastq files"
             
             }
     

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"
+  viash_version: "0.9.0"
-  git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724"
+  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"

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
+// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
-// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
+// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
-// Data Intuitive.
+// 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(";")
+              def split = renameString.split(":")
-              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              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",
+    "viash_version" : "0.9.0",
-    "git_commit" : "b84b29747d0635f2ac83ea63b496be9a9edb6724",
+    "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
+unset_if_false=(
-[[ "\\$par_dirs" == "false" ]] && unset par_dirs
+    par_ignore_symlinks
-[[ "\\$par_full_names" == "false" ]] && unset par_full_names
+    par_dirs
-[[ "\\$par_fn_as_s_name" == "false" ]] && unset par_fn_as_s_name
+    par_full_names
-[[ "\\$par_profile_runtime" == "false" ]] && unset par_profile_runtime
+    par_fn_as_s_name
-[[ "\\$par_verbose" == "false" ]] && unset par_verbose
+    par_profile_runtime
-[[ "\\$par_quiet" == "false" ]] && unset par_quiet
+    par_verbose
-[[ "\\$par_strict" == "false" ]] && unset par_strict
+    par_quiet
-[[ "\\$par_development" == "false" ]] && unset par_development
+    par_strict
-[[ "\\$par_require_logs" == "false" ]] && unset par_require_logs
+    par_development
-[[ "\\$par_no_megaqc_upload" == "false" ]] && unset par_no_megaqc_upload
+    par_require_logs
-[[ "\\$par_no_ansi" == "false" ]] && unset par_no_ansi
+    par_no_megaqc_upload
-[[ "\\$par_flat" == "false" ]] && unset par_flat
+    par_no_ansi
-[[ "\\$par_interactive" == "false" ]] && unset par_interactive
+    par_flat
-[[ "\\$par_static_plot_export" == "false" ]] && unset par_static_plot_export
+    par_interactive
-[[ "\\$par_data_dir" == "false" ]] && unset par_data_dir
+    par_static_plot_export
-[[ "\\$par_no_data_dir" == "false" ]] && unset par_no_data_dir
+    par_data_dir
-[[ "\\$par_zip_data_dir" == "false" ]] && unset par_zip_data_dir
+    par_no_data_dir
-[[ "\\$par_pdf" == "false" ]] && unset par_pdf
+    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})"
+      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()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
+      "\n\${viash_par_${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"
 }'''),

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'

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",
+                "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"
+                "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",
+                "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"
+                "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",
+                "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"
+                "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: `\",\"`. ",
+                "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: `\",\"`. "
+                "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: `\",\"`. ",
+                "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: `\",\"`. "
+                "help_text": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. "
             
             }
     

target/executable/io/interop_summary_to_csv/.config.vsh.yaml

@@ -141,7 +141,7 @@ build_info:
   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"
-  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
+  git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"

target/executable/io/interop_summary_to_csv/interop_summary_to_csv

@@ -470,9 +470,9 @@ 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="2024-09-12T12:25:58Z"
+LABEL org.opencontainers.image.created="2024-09-13T09:38:22Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
+LABEL org.opencontainers.image.revision="399e46901d6ce882a7430842b0d74774736439e2"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/io/untar/.config.vsh.yaml

@@ -148,7 +148,7 @@ build_info:
   output: "target/executable/io/untar"
   executable: "target/executable/io/untar/untar"
   viash_version: "0.9.0"
-  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
+  git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"

target/executable/io/untar/untar

@@ -476,9 +476,9 @@ 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="2024-09-12T12:25:58Z"
+LABEL org.opencontainers.image.created="2024-09-13T09:38:22Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
+LABEL org.opencontainers.image.revision="399e46901d6ce882a7430842b0d74774736439e2"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/nextflow/dataflow/combine_samples/.config.vsh.yaml

@@ -139,7 +139,7 @@ build_info:
   output: "target/nextflow/dataflow/combine_samples"
   executable: "target/nextflow/dataflow/combine_samples/main.nf"
   viash_version: "0.9.0"
-  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
+  git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"

target/nextflow/dataflow/combine_samples/main.nf

@@ -2972,7 +2972,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/combine_samples",
     "viash_version" : "0.9.0",
-    "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
+    "git_commit" : "399e46901d6ce882a7430842b0d74774736439e2",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {

target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml

@@ -133,7 +133,7 @@ build_info:
   output: "target/nextflow/dataflow/gather_fastqs_and_validate"
   executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
   viash_version: "0.9.0"
-  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
+  git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"

target/nextflow/dataflow/gather_fastqs_and_validate/main.nf

@@ -2965,7 +2965,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
     "viash_version" : "0.9.0",
-    "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
+    "git_commit" : "399e46901d6ce882a7430842b0d74774736439e2",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {

target/nextflow/demultiplex/.config.vsh.yaml

@@ -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"
@@ -186,16 +186,16 @@ build_info:
   output: "target/nextflow/demultiplex"
   executable: "target/nextflow/demultiplex/main.nf"
   viash_version: "0.9.0"
-  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
+  git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
   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/v0.2.0/nextflow/bcl_convert"
-  - "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco"
-  - "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc"
 package_config:
   name: "demultiplex"
   version: "main"

target/nextflow/demultiplex/main.nf

@@ -2932,7 +2932,7 @@ meta = [
       "repository" : {
         "type" : "vsh",
         "repo" : "biobox",
-        "tag" : "v0.1.0"
+        "tag" : "v0.2.0"
       }
     },
     {
@@ -2940,7 +2940,7 @@ meta = [
       "repository" : {
         "type" : "vsh",
         "repo" : "biobox",
-        "tag" : "v0.1.0"
+        "tag" : "v0.2.0"
       }
     },
     {
@@ -2948,7 +2948,7 @@ meta = [
       "repository" : {
         "type" : "vsh",
         "repo" : "biobox",
-        "tag" : "v0.1.0"
+        "tag" : "v0.2.0"
       }
     }
   ],
@@ -2957,7 +2957,7 @@ meta = [
       "type" : "vsh",
       "name" : "bb",
       "repo" : "biobox",
-      "tag" : "v0.1.0"
+      "tag" : "v0.2.0"
     }
   ],
   "license" : "MIT",
@@ -3049,7 +3049,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/demultiplex",
     "viash_version" : "0.9.0",
-    "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
+    "git_commit" : "399e46901d6ce882a7430842b0d74774736439e2",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {
@@ -3095,9 +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 "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/main.nf"
+include { bcl_convert } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/bcl_convert/main.nf"
-include { falco } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/main.nf"
+include { falco } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/falco/main.nf"
-include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/main.nf"
+include { multiqc } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf"
 
 // inner workflow
 // user-provided Nextflow code

target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml

@@ -141,7 +141,7 @@ build_info:
   output: "target/nextflow/io/interop_summary_to_csv"
   executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
   viash_version: "0.9.0"
-  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
+  git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"

target/nextflow/io/interop_summary_to_csv/main.nf

@@ -2977,7 +2977,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/interop_summary_to_csv",
     "viash_version" : "0.9.0",
-    "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
+    "git_commit" : "399e46901d6ce882a7430842b0d74774736439e2",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {

target/nextflow/io/untar/.config.vsh.yaml

@@ -148,7 +148,7 @@ build_info:
   output: "target/nextflow/io/untar"
   executable: "target/nextflow/io/untar/main.nf"
   viash_version: "0.9.0"
-  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
+  git_commit: "399e46901d6ce882a7430842b0d74774736439e2"
   git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
   name: "demultiplex"

target/nextflow/io/untar/main.nf

@@ -2989,7 +2989,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/untar",
     "viash_version" : "0.9.0",
-    "git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
+    "git_commit" : "399e46901d6ce882a7430842b0d74774736439e2",
     "git_remote" : "https://github.com/viash-hub/demultiplex"
   },
   "package_config" : {

test_resources

@@ -1 +0,0 @@
-/work/viash_hub_resources/viash-hub/demultiplex/ebb861b02ab66db004c32fa46573bb1e/200624_A00834_0183_BHMTFYDRXX.tar.gz