Build branch v0.1 with version v0.1.0 (3143dd6)

Build pipeline: viash-hub.craftbox.v0.1-6rdzs Source commit: 3143dd6e4c Source message: (Re-) release v0.1.0l
2024-09-12 16:01:34 +00:00
parent 9d767f2ae3
commit a51c8bef71
18 changed files with 166 additions and 132 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,4 @@
-# craftbox x.x.x
+# craftbox 0.1.0

 ## NEW FEATURES

--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,4 +1,5 @@
 name: craftbox
+version: v0.1.0
 description: |
  A collection of custom-tailored scripts and applied tools.
 license: MIT
@@ -7,7 +8,7 @@ links:
  issue_tracker: https://github.com/viash-hub/craftbox/issues
  repository: https://github.com/viash-hub/craftbox

-viash_version: 0.9.0-RC7
+viash_version: 0.9.0

 config_mods: |
  .requirements.commands := ['ps']
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,6 +1,6 @@
 manifest {
  name = "craftbox"
-  version = "v0.1"
+  version = "v0.1.0"
  defaultBranch = "main"
  nextflowVersion = "!>=20.12.1-edge"
 }
--- a/target/executable/concat_text/.config.vsh.yaml
+++ b/target/executable/concat_text/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "concat_text"
-version: "v0.1"
+version: "v0.1.0"
 authors:
 - name: "Toni Verbeiren"
  roles:
@@ -152,7 +152,7 @@ engines:
  id: "docker"
  image: "alpine:latest"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1"
+  target_tag: "v0.1.0"
  namespace_separator: "/"
  setup:
  - type: "apk"
@@ -170,22 +170,22 @@ build_info:
  engine: "docker|native"
  output: "target/executable/concat_text"
  executable: "target/executable/concat_text/concat_text"
-  viash_version: "0.9.0-RC7"
-  git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
+  viash_version: "0.9.0"
+  git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
-  version: "v0.1"
+  version: "v0.1.0"
  description: "A collection of custom-tailored scripts and applied tools.\n"
  info: null
-  viash_version: "0.9.0-RC7"
+  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'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/executable/concat_text/concat_text
+++ b/target/executable/concat_text/concat_text
@@ -1,10 +1,10 @@
 #!/usr/bin/env bash

-# concat_text v0.1
+# concat_text v0.1.0
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 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
@@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "concat_text v0.1"
+  echo "concat_text v0.1.0"
  echo ""
  echo "Concatenate a number of text files, handle gzipped text files gracefully and"
  echo "optionally gzip the output text file."
@@ -479,10 +479,10 @@ RUN apk add --no-cache bash procps file

 LABEL org.opencontainers.image.authors="Toni Verbeiren, Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component concat_text"
-LABEL org.opencontainers.image.created="2024-09-12T15:43:28Z"
+LABEL org.opencontainers.image.created="2024-09-12T15:57:23Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
-LABEL org.opencontainers.image.version="v0.1"
+LABEL org.opencontainers.image.revision="3143dd6e4c2c3107f79639fe8602d92f3141ad82"
+LABEL org.opencontainers.image.version="v0.1.0"

 VIASHDOCKER
  fi
@@ -618,7 +618,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "concat_text v0.1"
+            echo "concat_text v0.1.0"
            exit
            ;;
        --input)
@@ -742,7 +742,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/concat_text:v0.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/concat_text:v0.1.0'
  fi

  # print dockerfile
--- a/target/executable/csv2fasta/.config.vsh.yaml
+++ b/target/executable/csv2fasta/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "csv2fasta"
-version: "v0.1"
+version: "v0.1.0"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -192,7 +192,7 @@ engines:
  id: "docker"
  image: "python:slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1"
+  target_tag: "v0.1.0"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -221,22 +221,22 @@ build_info:
  engine: "docker|native"
  output: "target/executable/csv2fasta"
  executable: "target/executable/csv2fasta/csv2fasta"
-  viash_version: "0.9.0-RC7"
-  git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
+  viash_version: "0.9.0"
+  git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
-  version: "v0.1"
+  version: "v0.1.0"
  description: "A collection of custom-tailored scripts and applied tools.\n"
  info: null
-  viash_version: "0.9.0-RC7"
+  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'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/executable/csv2fasta/csv2fasta
+++ b/target/executable/csv2fasta/csv2fasta
@@ -1,10 +1,10 @@
 #!/usr/bin/env bash

-# csv2fasta v0.1
+# csv2fasta v0.1.0
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "csv2fasta v0.1"
+  echo "csv2fasta v0.1.0"
  echo ""
  echo "Convert two columns from a CSV file to FASTA entries. The CSV file can"
  echo "contain an optional header and each row (other than the header) becomes"
@@ -525,10 +525,10 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "dnaio"

 LABEL org.opencontainers.image.description="Companion container for running component csv2fasta"
-LABEL org.opencontainers.image.created="2024-09-12T15:43:27Z"
+LABEL org.opencontainers.image.created="2024-09-12T15:57:22Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
-LABEL org.opencontainers.image.version="v0.1"
+LABEL org.opencontainers.image.revision="3143dd6e4c2c3107f79639fe8602d92f3141ad82"
+LABEL org.opencontainers.image.version="v0.1.0"

 VIASHDOCKER
  fi
@@ -664,7 +664,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "csv2fasta v0.1"
+            echo "csv2fasta v0.1.0"
            exit
            ;;
        --input)
@@ -848,7 +848,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/csv2fasta:v0.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/csv2fasta:v0.1.0'
  fi

  # print dockerfile
--- a/target/executable/untar/.config.vsh.yaml
+++ b/target/executable/untar/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "untar"
-version: "v0.1"
+version: "v0.1.0"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -129,7 +129,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1"
+  target_tag: "v0.1.0"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -146,22 +146,22 @@ build_info:
  engine: "docker|native"
  output: "target/executable/untar"
  executable: "target/executable/untar/untar"
-  viash_version: "0.9.0-RC7"
-  git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
+  viash_version: "0.9.0"
+  git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
-  version: "v0.1"
+  version: "v0.1.0"
  description: "A collection of custom-tailored scripts and applied tools.\n"
  info: null
-  viash_version: "0.9.0-RC7"
+  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'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/executable/untar/untar
+++ b/target/executable/untar/untar
@@ -1,10 +1,10 @@
 #!/usr/bin/env bash

-# untar v0.1
+# untar v0.1.0
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC7 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "untar v0.1"
+  echo "untar v0.1.0"
  echo ""
  echo "Unpack a .tar file. When the contents of the .tar file is just a single"
  echo "directory,"
@@ -476,10 +476,10 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component untar"
-LABEL org.opencontainers.image.created="2024-09-12T15:43:28Z"
+LABEL org.opencontainers.image.created="2024-09-12T15:57:22Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
-LABEL org.opencontainers.image.version="v0.1"
+LABEL org.opencontainers.image.revision="3143dd6e4c2c3107f79639fe8602d92f3141ad82"
+LABEL org.opencontainers.image.version="v0.1.0"

 VIASHDOCKER
  fi
@@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "untar v0.1"
+            echo "untar v0.1.0"
            exit
            ;;
        --input)
@@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/untar:v0.1'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/untar:v0.1.0'
  fi

  # print dockerfile
--- a/target/nextflow/concat_text/.config.vsh.yaml
+++ b/target/nextflow/concat_text/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "concat_text"
-version: "v0.1"
+version: "v0.1.0"
 authors:
 - name: "Toni Verbeiren"
  roles:
@@ -152,7 +152,7 @@ engines:
  id: "docker"
  image: "alpine:latest"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1"
+  target_tag: "v0.1.0"
  namespace_separator: "/"
  setup:
  - type: "apk"
@@ -170,22 +170,22 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/concat_text"
  executable: "target/nextflow/concat_text/main.nf"
-  viash_version: "0.9.0-RC7"
-  git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
+  viash_version: "0.9.0"
+  git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
-  version: "v0.1"
+  version: "v0.1.0"
  description: "A collection of custom-tailored scripts and applied tools.\n"
  info: null
-  viash_version: "0.9.0-RC7"
+  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'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/nextflow/concat_text/main.nf
+++ b/target/nextflow/concat_text/main.nf
@@ -1,8 +1,8 @@
-// concat_text v0.1
+// concat_text v0.1.0
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC7 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
@@ -1732,7 +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_?

@@ -1803,7 +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
@@ -1845,7 +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
@@ -2803,7 +2809,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "concat_text",
-  "version" : "v0.1",
+  "version" : "v0.1.0",
  "authors" : [
    {
      "name" : "Toni Verbeiren",
@@ -3001,7 +3007,7 @@ meta = [
      "id" : "docker",
      "image" : "alpine:latest",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1",
+      "target_tag" : "v0.1.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3024,22 +3030,22 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/concat_text",
-    "viash_version" : "0.9.0-RC7",
-    "git_commit" : "5705b88fa20f267475b5d0ae1ca25dbf55ff1295",
+    "viash_version" : "0.9.0",
+    "git_commit" : "3143dd6e4c2c3107f79639fe8602d92f3141ad82",
    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
-    "version" : "v0.1",
+    "version" : "v0.1.0",
    "description" : "A collection of custom-tailored scripts and applied tools.\n",
-    "viash_version" : "0.9.0-RC7",
+    "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'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
    ],
    "keywords" : [
      "scripts",
@@ -3204,7 +3210,11 @@ 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]
          }
@@ -3335,7 +3345,8 @@ 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")

@@ -3343,8 +3354,8 @@ 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!
@@ -3381,6 +3392,7 @@ 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)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3392,10 +3404,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  |$stub
  |\"\"\"
  |script:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
  |def parInject = args
  |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
  |  .join("\\n")
  |\"\"\"
  |# meta exports
@@ -3480,7 +3491,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/craftbox/concat_text",
-    "tag" : "v0.1"
+    "tag" : "v0.1.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/concat_text/nextflow.config
+++ b/target/nextflow/concat_text/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'concat_text'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1'
+  version = 'v0.1.0'
  description = 'Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n'
  author = 'Toni Verbeiren, Dries Schaumont'
 }
--- a/target/nextflow/csv2fasta/.config.vsh.yaml
+++ b/target/nextflow/csv2fasta/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "csv2fasta"
-version: "v0.1"
+version: "v0.1.0"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -192,7 +192,7 @@ engines:
  id: "docker"
  image: "python:slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1"
+  target_tag: "v0.1.0"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -221,22 +221,22 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/csv2fasta"
  executable: "target/nextflow/csv2fasta/main.nf"
-  viash_version: "0.9.0-RC7"
-  git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
+  viash_version: "0.9.0"
+  git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
-  version: "v0.1"
+  version: "v0.1.0"
  description: "A collection of custom-tailored scripts and applied tools.\n"
  info: null
-  viash_version: "0.9.0-RC7"
+  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'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/nextflow/csv2fasta/main.nf
+++ b/target/nextflow/csv2fasta/main.nf
@@ -1,8 +1,8 @@
-// csv2fasta v0.1
+// csv2fasta v0.1.0
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC7 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
@@ -1728,7 +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_?

@@ -1799,7 +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
@@ -1841,7 +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
@@ -2799,7 +2805,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "csv2fasta",
-  "version" : "v0.1",
+  "version" : "v0.1.0",
  "argument_groups" : [
    {
      "name" : "Inputs",
@@ -3019,7 +3025,7 @@ meta = [
      "id" : "docker",
      "image" : "python:slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1",
+      "target_tag" : "v0.1.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3060,22 +3066,22 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/csv2fasta",
-    "viash_version" : "0.9.0-RC7",
-    "git_commit" : "5705b88fa20f267475b5d0ae1ca25dbf55ff1295",
+    "viash_version" : "0.9.0",
+    "git_commit" : "3143dd6e4c2c3107f79639fe8602d92f3141ad82",
    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
-    "version" : "v0.1",
+    "version" : "v0.1.0",
    "description" : "A collection of custom-tailored scripts and applied tools.\n",
-    "viash_version" : "0.9.0-RC7",
+    "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'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
    ],
    "keywords" : [
      "scripts",
@@ -3316,7 +3322,11 @@ 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]
          }
@@ -3447,7 +3457,8 @@ 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")

@@ -3455,8 +3466,8 @@ 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!
@@ -3493,6 +3504,7 @@ 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)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3504,10 +3516,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  |$stub
  |\"\"\"
  |script:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
  |def parInject = args
  |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
  |  .join("\\n")
  |\"\"\"
  |# meta exports
@@ -3592,7 +3603,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/craftbox/csv2fasta",
-    "tag" : "v0.1"
+    "tag" : "v0.1.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/csv2fasta/nextflow.config
+++ b/target/nextflow/csv2fasta/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'csv2fasta'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1'
+  version = 'v0.1.0'
  description = 'Convert two columns from a CSV file to FASTA entries. The CSV file can\ncontain an optional header and each row (other than the header) becomes\na single FASTA record. One of the two columns will be used as the names\nfor the FASTA entries, while the other become the sequences. The sequences\ncolumn must only contain characters that are valid IUPAC notation for \nnucleotides or a group thereof (wildcard characters).\n'
 }

--- a/target/nextflow/untar/.config.vsh.yaml
+++ b/target/nextflow/untar/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "untar"
-version: "v0.1"
+version: "v0.1.0"
 argument_groups:
 - name: "Input arguments"
  arguments:
@@ -129,7 +129,7 @@ engines:
  id: "docker"
  image: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1"
+  target_tag: "v0.1.0"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -146,22 +146,22 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/untar"
  executable: "target/nextflow/untar/main.nf"
-  viash_version: "0.9.0-RC7"
-  git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
+  viash_version: "0.9.0"
+  git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
-  version: "v0.1"
+  version: "v0.1.0"
  description: "A collection of custom-tailored scripts and applied tools.\n"
  info: null
-  viash_version: "0.9.0-RC7"
+  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'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
  keywords:
  - "scripts"
  - "custom"
--- a/target/nextflow/untar/main.nf
+++ b/target/nextflow/untar/main.nf
@@ -1,8 +1,8 @@
-// untar v0.1
+// untar v0.1.0
 // 
-// This wrapper script is auto-generated by viash 0.9.0-RC7 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
@@ -1728,7 +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_?

@@ -1799,7 +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
@@ -1841,7 +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
@@ -2799,7 +2805,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "untar",
-  "version" : "v0.1",
+  "version" : "v0.1.0",
  "argument_groups" : [
    {
      "name" : "Input arguments",
@@ -2959,7 +2965,7 @@ meta = [
      "id" : "docker",
      "image" : "debian:stable-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1",
+      "target_tag" : "v0.1.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -2981,22 +2987,22 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/untar",
-    "viash_version" : "0.9.0-RC7",
-    "git_commit" : "5705b88fa20f267475b5d0ae1ca25dbf55ff1295",
+    "viash_version" : "0.9.0",
+    "git_commit" : "3143dd6e4c2c3107f79639fe8602d92f3141ad82",
    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
-    "version" : "v0.1",
+    "version" : "v0.1.0",
    "description" : "A collection of custom-tailored scripts and applied tools.\n",
-    "viash_version" : "0.9.0-RC7",
+    "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'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
    ],
    "keywords" : [
      "scripts",
@@ -3167,7 +3173,11 @@ 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]
          }
@@ -3298,7 +3308,8 @@ 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")

@@ -3306,8 +3317,8 @@ 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!
@@ -3344,6 +3355,7 @@ 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)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
@@ -3355,10 +3367,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  |$stub
  |\"\"\"
  |script:$assertStr
-  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
  |def parInject = args
  |  .findAll{key, value -> value != null}
-  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"}
  |  .join("\\n")
  |\"\"\"
  |# meta exports
@@ -3443,7 +3454,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/craftbox/untar",
-    "tag" : "v0.1"
+    "tag" : "v0.1.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/nextflow/untar/nextflow.config
+++ b/target/nextflow/untar/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'untar'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1'
+  version = 'v0.1.0'
  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'
 }