Build branch main with version main (3fecd6a)

Build pipeline: viash-hub.craftbox.main-62xgd Source commit: 3fecd6a214 Source message: Update CHANGELOG
2024-09-12 16:02:59 +00:00
parent 108879b9f9
commit 3f8933e831
14 changed files with 104 additions and 71 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
@@ -7,7 +7,7 @@ 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/target/executable/concat_text/.config.vsh.yaml
+++ b/target/executable/concat_text/.config.vsh.yaml
@@ -170,15 +170,15 @@ 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: "3fecd6a214295592c65d5ef03b8b7115867f8752"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
  version: "main"
  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:
--- a/target/executable/concat_text/concat_text
+++ b/target/executable/concat_text/concat_text
@@ -2,9 +2,9 @@

 # concat_text main
 # 
-# 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
@@ -479,9 +479,9 @@ 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="2024-09-12T15:41:16Z"
+LABEL org.opencontainers.image.created="2024-09-12T15:58:08Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
+LABEL org.opencontainers.image.revision="3fecd6a214295592c65d5ef03b8b7115867f8752"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/csv2fasta/.config.vsh.yaml
+++ b/target/executable/csv2fasta/.config.vsh.yaml
@@ -221,15 +221,15 @@ 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: "3fecd6a214295592c65d5ef03b8b7115867f8752"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
  version: "main"
  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:
--- a/target/executable/csv2fasta/csv2fasta
+++ b/target/executable/csv2fasta/csv2fasta
@@ -2,9 +2,9 @@

 # csv2fasta main
 # 
-# 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
@@ -525,9 +525,9 @@ 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="2024-09-12T15:41:15Z"
+LABEL org.opencontainers.image.created="2024-09-12T15:58:07Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
+LABEL org.opencontainers.image.revision="3fecd6a214295592c65d5ef03b8b7115867f8752"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/untar/.config.vsh.yaml
+++ b/target/executable/untar/.config.vsh.yaml
@@ -146,15 +146,15 @@ 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: "3fecd6a214295592c65d5ef03b8b7115867f8752"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
  version: "main"
  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:
--- a/target/executable/untar/untar
+++ b/target/executable/untar/untar
@@ -2,9 +2,9 @@

 # untar main
 # 
-# 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
@@ -476,9 +476,9 @@ 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="2024-09-12T15:41:15Z"
+LABEL org.opencontainers.image.created="2024-09-12T15:58:07Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
+LABEL org.opencontainers.image.revision="3fecd6a214295592c65d5ef03b8b7115867f8752"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/nextflow/concat_text/.config.vsh.yaml
+++ b/target/nextflow/concat_text/.config.vsh.yaml
@@ -170,15 +170,15 @@ 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: "3fecd6a214295592c65d5ef03b8b7115867f8752"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
  version: "main"
  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:
--- a/target/nextflow/concat_text/main.nf
+++ b/target/nextflow/concat_text/main.nf
@@ -1,8 +1,8 @@
 // concat_text main
 // 
-// 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
@@ -3024,15 +3030,15 @@ 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" : "3fecd6a214295592c65d5ef03b8b7115867f8752",
    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
    "version" : "main",
    "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" : [
@@ -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
--- a/target/nextflow/csv2fasta/.config.vsh.yaml
+++ b/target/nextflow/csv2fasta/.config.vsh.yaml
@@ -221,15 +221,15 @@ 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: "3fecd6a214295592c65d5ef03b8b7115867f8752"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
  version: "main"
  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:
--- a/target/nextflow/csv2fasta/main.nf
+++ b/target/nextflow/csv2fasta/main.nf
@@ -1,8 +1,8 @@
 // csv2fasta main
 // 
-// 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
@@ -3060,15 +3066,15 @@ 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" : "3fecd6a214295592c65d5ef03b8b7115867f8752",
    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
    "version" : "main",
    "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" : [
@@ -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
--- a/target/nextflow/untar/.config.vsh.yaml
+++ b/target/nextflow/untar/.config.vsh.yaml
@@ -146,15 +146,15 @@ 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: "3fecd6a214295592c65d5ef03b8b7115867f8752"
  git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
  name: "craftbox"
  version: "main"
  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:
--- a/target/nextflow/untar/main.nf
+++ b/target/nextflow/untar/main.nf
@@ -1,8 +1,8 @@
 // untar main
 // 
-// 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
@@ -2981,15 +2987,15 @@ 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" : "3fecd6a214295592c65d5ef03b8b7115867f8752",
    "git_remote" : "https://github.com/viash-hub/craftbox"
  },
  "package_config" : {
    "name" : "craftbox",
    "version" : "main",
    "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" : [
@@ -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