Build branch main with version main (9f37358)

Build pipeline: viash-hub.demultiplex.main-f597w Source commit: 9f37358ebf Source message: Minor adjustments to CHANGELOG and README (#45)
2025-04-25 12:20:54 +00:00
parent eb6fd9e999
commit 60ee0cd261
30 changed files with 388 additions and 411 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,8 +1,14 @@
 # demultiplex v0.3.9

+## Bug fixes
+
+* Fix defaults for output arguments in nextflow schema's.
+
+* Fix an issue where an integer being passed to a argument with `type: double` resulted in an error (PR #44).
+
 ## Minor changes

-* Bump viash to 0.9.3 (PR #43).
+* Bump viash to 0.9.4, which adds support for nextflow versions starting major version 25.01 (PR #43 and #44).

 # demultiplex v0.3.8

--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@ License](https://img.shields.io/github/license/viash-hub/demultiplex.svg)](https
 [![GitHub
 Issues](https://img.shields.io/github/issues/viash-hub/demultiplex.svg)](https://github.com/viash-hub/demultiplex/issues)
 [![Viash
-version](https://img.shields.io/badge/Viash-v0.9.1-blue)](https://viash.io)
+version](https://img.shields.io/badge/Viash-v0.9.4-blue)](https://viash.io)

 ## Workflow Overview
 The workflow executes the following steps: 
@@ -53,7 +53,7 @@ You can check if everything is working by getting the `--help` for a workflow:
 ```bash
 nextflow run \
 vsh/demultiplex \
-r v0.3.4 \
+-r v0.3.9 \
 --help
 ```

@@ -84,7 +84,7 @@ When starting nextflow using the CLI, you can use `-c` to provide the file to ne

 ```bash
 nextflow run vsh/demultiplex \
-r v0.3.4 \
+-r v0.3.9 \
 -main-script target/nextflow/runner/main.nf \
 --input "gs://viash-hub-test-data/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2"  \
 --demultiplexer bclconvert \
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -11,10 +11,10 @@ info:
    - path: gs://viash-hub-test-data/demultiplex/v2/
      dest: testData

-viash_version: 0.9.3
+viash_version: 0.9.4

 config_mods: |
-  .requirements.commands := ['ps']
+  .requirements.commands += ['ps']
  .runners[.type == 'nextflow'].directives.tag := '$id'
  .resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}
  .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -48,6 +48,8 @@ scope:
  target: "public"
 requirements:
  commands:
+  - "summary"
+  - "index-summary"
  - "ps"
 license: "MIT"
 links:
@@ -148,10 +150,10 @@ build_info:
  engine: "docker|native"
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
-  viash_version: "0.9.3"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  viash_version: "0.9.4"
+  git_commit: "9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-22-g162497a"
+  git_tag: "v0.1.1-24-g9f37358"
 package_config:
  name: "demultiplex"
  version: "main"
@@ -160,11 +162,11 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/demultiplex/v2/"
      dest: "testData"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
+  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'\n"
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -2,7 +2,7 @@

 # interop_summary_to_csv main
 # 
-# This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -454,9 +454,9 @@ 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="2025-04-22T11:54:46Z"
+LABEL org.opencontainers.image.created="2025-04-25T12:07:26Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="162497ab73faf321d5166fe34cd1f6976b14dcb0"
+LABEL org.opencontainers.image.revision="9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -781,13 +781,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # build docker image
  elif [ "$VIASH_MODE" == "setup" ]; then
    ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
-    ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
+    ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'summary' 'index-summary' 'ps' 'bash'
    exit 0
  fi

  # check if docker image exists
  ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
-  ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
+  ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'summary' 'index-summary' 'ps' 'bash'
 fi

 # setting computational defaults
--- a/target/executable/io/publish/.config.vsh.yaml
+++ b/target/executable/io/publish/.config.vsh.yaml
@@ -198,10 +198,10 @@ build_info:
  engine: "docker|native"
  output: "target/executable/io/publish"
  executable: "target/executable/io/publish/publish"
-  viash_version: "0.9.3"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  viash_version: "0.9.4"
+  git_commit: "9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-22-g162497a"
+  git_tag: "v0.1.1-24-g9f37358"
 package_config:
  name: "demultiplex"
  version: "main"
@@ -210,11 +210,11 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/demultiplex/v2/"
      dest: "testData"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
+  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'\n"
--- a/target/executable/io/publish/publish
+++ b/target/executable/io/publish/publish
@@ -2,7 +2,7 @@

 # publish main
 # 
-# This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -450,9 +450,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io publish"
-LABEL org.opencontainers.image.created="2025-04-22T11:54:46Z"
+LABEL org.opencontainers.image.created="2025-04-25T12:07:25Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="162497ab73faf321d5166fe34cd1f6976b14dcb0"
+LABEL org.opencontainers.image.revision="9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -155,10 +155,10 @@ build_info:
  engine: "docker|native"
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
-  viash_version: "0.9.3"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  viash_version: "0.9.4"
+  git_commit: "9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-22-g162497a"
+  git_tag: "v0.1.1-24-g9f37358"
 package_config:
  name: "demultiplex"
  version: "main"
@@ -167,11 +167,11 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/demultiplex/v2/"
      dest: "testData"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
+  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'\n"
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -2,7 +2,7 @@

 # untar main
 # 
-# This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -450,9 +450,9 @@ 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="2025-04-22T11:54:46Z"
+LABEL org.opencontainers.image.created="2025-04-25T12:07:25Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="162497ab73faf321d5166fe34cd1f6976b14dcb0"
+LABEL org.opencontainers.image.revision="9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
+++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml
@@ -164,10 +164,10 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/dataflow/combine_samples"
  executable: "target/nextflow/dataflow/combine_samples/main.nf"
-  viash_version: "0.9.3"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  viash_version: "0.9.4"
+  git_commit: "9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-22-g162497a"
+  git_tag: "v0.1.1-24-g9f37358"
 package_config:
  name: "demultiplex"
  version: "main"
@@ -176,11 +176,11 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/demultiplex/v2/"
      dest: "testData"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
+  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'\n"
--- a/target/nextflow/dataflow/combine_samples/main.nf
+++ b/target/nextflow/dataflow/combine_samples/main.nf
@@ -1,6 +1,6 @@
 // combine_samples main
 // 
-// This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3234,10 +3229,10 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/combine_samples",
-    "viash_version" : "0.9.3",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "viash_version" : "0.9.4",
+    "git_commit" : "9f37358ebfc77012c8c0dedd79a40e27b121c6c1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-22-g162497a"
+    "git_tag" : "v0.1.1-24-g9f37358"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3251,11 +3246,11 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.3",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main'"
--- a/target/nextflow/dataflow/combine_samples/nextflow_schema.json
+++ b/target/nextflow/dataflow/combine_samples/nextflow_schema.json
@@ -67,10 +67,10 @@
                "output_forward": {
                "type":
                "string",
-                "description": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\";\"`. ",
-                "help_text": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\";\"`. "
+                "description": "Type: List of `file`, required, default: `$id.$key.output_forward_*`, multiple_sep: `\";\"`. ",
+                "help_text": "Type: List of `file`, required, default: `$id.$key.output_forward_*`, multiple_sep: `\";\"`. "
            ,
-                "default":"$id.$key.output_forward_*.output_forward_*"
+                "default":"$id.$key.output_forward_*"
            }
    

@@ -78,10 +78,10 @@
                "output_reverse": {
                "type":
                "string",
-                "description": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\";\"`. ",
-                "help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\";\"`. "
+                "description": "Type: List of `file`, default: `$id.$key.output_reverse_*`, multiple_sep: `\";\"`. ",
+                "help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*`, multiple_sep: `\";\"`. "
            ,
-                "default":"$id.$key.output_reverse_*.output_reverse_*"
+                "default":"$id.$key.output_reverse_*"
            }
    

@@ -89,10 +89,10 @@
                "output_falco": {
                "type":
                "string",
-                "description": "Type: List of `file`, required, default: `$id.$key.output_falco_*.output_falco_*`, multiple_sep: `\";\"`. ",
-                "help_text": "Type: List of `file`, required, default: `$id.$key.output_falco_*.output_falco_*`, multiple_sep: `\";\"`. "
+                "description": "Type: List of `file`, required, default: `$id.$key.output_falco_*`, multiple_sep: `\";\"`. ",
+                "help_text": "Type: List of `file`, required, default: `$id.$key.output_falco_*`, multiple_sep: `\";\"`. "
            ,
-                "default":"$id.$key.output_falco_*.output_falco_*"
+                "default":"$id.$key.output_falco_*"
            }
    

--- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
@@ -140,10 +140,10 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/dataflow/gather_fastqs_and_validate"
  executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
-  viash_version: "0.9.3"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  viash_version: "0.9.4"
+  git_commit: "9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-22-g162497a"
+  git_tag: "v0.1.1-24-g9f37358"
 package_config:
  name: "demultiplex"
  version: "main"
@@ -152,11 +152,11 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/demultiplex/v2/"
      dest: "testData"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
+  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'\n"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
@@ -1,6 +1,6 @@
 // gather_fastqs_and_validate main
 // 
-// This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3207,10 +3202,10 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
-    "viash_version" : "0.9.3",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "viash_version" : "0.9.4",
+    "git_commit" : "9f37358ebfc77012c8c0dedd79a40e27b121c6c1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-22-g162497a"
+    "git_tag" : "v0.1.1-24-g9f37358"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3224,11 +3219,11 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.3",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main'"
--- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow_schema.json
+++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow_schema.json
@@ -47,10 +47,10 @@
                "fastq_forward": {
                "type":
                "string",
-                "description": "Type: List of `file`, required, default: `$id.$key.fastq_forward_*.fastq_forward_*`, multiple_sep: `\";\"`. ",
-                "help_text": "Type: List of `file`, required, default: `$id.$key.fastq_forward_*.fastq_forward_*`, multiple_sep: `\";\"`. "
+                "description": "Type: List of `file`, required, default: `$id.$key.fastq_forward_*`, multiple_sep: `\";\"`. ",
+                "help_text": "Type: List of `file`, required, default: `$id.$key.fastq_forward_*`, multiple_sep: `\";\"`. "
            ,
-                "default":"$id.$key.fastq_forward_*.fastq_forward_*"
+                "default":"$id.$key.fastq_forward_*"
            }
    

@@ -58,10 +58,10 @@
                "fastq_reverse": {
                "type":
                "string",
-                "description": "Type: List of `file`, default: `$id.$key.fastq_reverse_*.fastq_reverse_*`, multiple_sep: `\";\"`. ",
-                "help_text": "Type: List of `file`, default: `$id.$key.fastq_reverse_*.fastq_reverse_*`, multiple_sep: `\";\"`. "
+                "description": "Type: List of `file`, default: `$id.$key.fastq_reverse_*`, multiple_sep: `\";\"`. ",
+                "help_text": "Type: List of `file`, default: `$id.$key.fastq_reverse_*`, multiple_sep: `\";\"`. "
            ,
-                "default":"$id.$key.fastq_reverse_*.fastq_reverse_*"
+                "default":"$id.$key.fastq_reverse_*"
            }
    

--- a/target/nextflow/demultiplex/.config.vsh.yaml
+++ b/target/nextflow/demultiplex/.config.vsh.yaml
@@ -246,10 +246,10 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/demultiplex"
  executable: "target/nextflow/demultiplex/main.nf"
-  viash_version: "0.9.3"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  viash_version: "0.9.4"
+  git_commit: "9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-22-g162497a"
+  git_tag: "v0.1.1-24-g9f37358"
  dependencies:
  - "target/nextflow/io/untar"
  - "target/nextflow/dataflow/gather_fastqs_and_validate"
@@ -267,11 +267,11 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/demultiplex/v2/"
      dest: "testData"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
+  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'\n"
--- a/target/nextflow/demultiplex/main.nf
+++ b/target/nextflow/demultiplex/main.nf
@@ -1,6 +1,6 @@
 // demultiplex main
 // 
-// This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3354,10 +3349,10 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/demultiplex",
-    "viash_version" : "0.9.3",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "viash_version" : "0.9.4",
+    "git_commit" : "9f37358ebfc77012c8c0dedd79a40e27b121c6c1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-22-g162497a"
+    "git_tag" : "v0.1.1-24-g9f37358"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3371,11 +3366,11 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.3",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main'"
--- a/target/nextflow/demultiplex/nextflow_schema.json
+++ b/target/nextflow/demultiplex/nextflow_schema.json
@@ -69,10 +69,10 @@
                "output": {
                "type":
                "string",
-                "description": "Type: `file`, default: `$id.$key.output.output`. Directory to write fastq data to",
-                "help_text": "Type: `file`, default: `$id.$key.output.output`. Directory to write fastq data to"
+                "description": "Type: `file`, default: `$id/fastq`. Directory to write fastq data to",
+                "help_text": "Type: `file`, default: `$id/fastq`. Directory to write fastq data to"
            ,
-                "default":"$id.$key.output.output"
+                "default":"$id/fastq"
            }
    

@@ -80,10 +80,10 @@
                "output_falco": {
                "type":
                "string",
-                "description": "Type: List of `file`, default: `$id.$key.output_falco_*.output_falco_*`, multiple_sep: `\";\"`. Directory to write falco output to",
-                "help_text": "Type: List of `file`, default: `$id.$key.output_falco_*.output_falco_*`, multiple_sep: `\";\"`. Directory to write falco output to"
+                "description": "Type: List of `file`, default: `$id/qc/fastqc`, multiple_sep: `\";\"`. Directory to write falco output to",
+                "help_text": "Type: List of `file`, default: `$id/qc/fastqc`, multiple_sep: `\";\"`. Directory to write falco output to"
            ,
-                "default":"$id.$key.output_falco_*.output_falco_*"
+                "default":"$id/qc/fastqc"
            }
    

@@ -91,10 +91,10 @@
                "output_multiqc": {
                "type":
                "string",
-                "description": "Type: `file`, default: `$id.$key.output_multiqc.html`. Directory to write falco output to",
-                "help_text": "Type: `file`, default: `$id.$key.output_multiqc.html`. Directory to write falco output to"
+                "description": "Type: `file`, default: `$id/qc/multiqc_report.html`. Directory to write falco output to",
+                "help_text": "Type: `file`, default: `$id/qc/multiqc_report.html`. Directory to write falco output to"
            ,
-                "default":"$id.$key.output_multiqc.html"
+                "default":"$id/qc/multiqc_report.html"
            }
    

@@ -102,10 +102,10 @@
                "output_run_information": {
                "type":
                "string",
-                "description": "Type: `file`, required, default: `$id.$key.output_run_information.csv`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.output_run_information.csv`. "
+                "description": "Type: `file`, required, default: `$id/run_information.csv`. ",
+                "help_text": "Type: `file`, required, default: `$id/run_information.csv`. "
            ,
-                "default":"$id.$key.output_run_information.csv"
+                "default":"$id/run_information.csv"
            }
    

--- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
@@ -48,6 +48,8 @@ scope:
  target: "public"
 requirements:
  commands:
+  - "summary"
+  - "index-summary"
  - "ps"
 license: "MIT"
 links:
@@ -148,10 +150,10 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/io/interop_summary_to_csv"
  executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
-  viash_version: "0.9.3"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  viash_version: "0.9.4"
+  git_commit: "9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-22-g162497a"
+  git_tag: "v0.1.1-24-g9f37358"
 package_config:
  name: "demultiplex"
  version: "main"
@@ -160,11 +162,11 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/demultiplex/v2/"
      dest: "testData"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
+  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'\n"
--- a/target/nextflow/io/interop_summary_to_csv/main.nf
+++ b/target/nextflow/io/interop_summary_to_csv/main.nf
@@ -1,6 +1,6 @@
 // interop_summary_to_csv main
 // 
-// This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3100,6 +3095,8 @@ meta = [
  },
  "requirements" : {
    "commands" : [
+      "summary",
+      "index-summary",
      "ps"
    ]
  },
@@ -3219,10 +3216,10 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/io/interop_summary_to_csv",
-    "viash_version" : "0.9.3",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "viash_version" : "0.9.4",
+    "git_commit" : "9f37358ebfc77012c8c0dedd79a40e27b121c6c1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-22-g162497a"
+    "git_tag" : "v0.1.1-24-g9f37358"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3236,11 +3233,11 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.3",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main'"
--- a/target/nextflow/io/interop_summary_to_csv/nextflow_schema.json
+++ b/target/nextflow/io/interop_summary_to_csv/nextflow_schema.json
@@ -37,10 +37,10 @@
                "output_run_summary": {
                "type":
                "string",
-                "description": "Type: `file`, required, default: `$id.$key.output_run_summary.output_run_summary`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.output_run_summary.output_run_summary`. "
+                "description": "Type: `file`, required, default: `$id.$key.output_run_summary`. ",
+                "help_text": "Type: `file`, required, default: `$id.$key.output_run_summary`. "
            ,
-                "default":"$id.$key.output_run_summary.output_run_summary"
+                "default":"$id.$key.output_run_summary"
            }
    

@@ -48,10 +48,10 @@
                "output_index_summary": {
                "type":
                "string",
-                "description": "Type: `file`, required, default: `$id.$key.output_index_summary.output_index_summary`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.output_index_summary.output_index_summary`. "
+                "description": "Type: `file`, required, default: `$id.$key.output_index_summary`. ",
+                "help_text": "Type: `file`, required, default: `$id.$key.output_index_summary`. "
            ,
-                "default":"$id.$key.output_index_summary.output_index_summary"
+                "default":"$id.$key.output_index_summary"
            }
    

--- a/target/nextflow/io/publish/.config.vsh.yaml
+++ b/target/nextflow/io/publish/.config.vsh.yaml
@@ -198,10 +198,10 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/io/publish"
  executable: "target/nextflow/io/publish/main.nf"
-  viash_version: "0.9.3"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  viash_version: "0.9.4"
+  git_commit: "9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-22-g162497a"
+  git_tag: "v0.1.1-24-g9f37358"
 package_config:
  name: "demultiplex"
  version: "main"
@@ -210,11 +210,11 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/demultiplex/v2/"
      dest: "testData"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
+  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'\n"
--- a/target/nextflow/io/publish/main.nf
+++ b/target/nextflow/io/publish/main.nf
@@ -1,6 +1,6 @@
 // publish main
 // 
-// This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3278,10 +3273,10 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish",
-    "viash_version" : "0.9.3",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "viash_version" : "0.9.4",
+    "git_commit" : "9f37358ebfc77012c8c0dedd79a40e27b121c6c1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-22-g162497a"
+    "git_tag" : "v0.1.1-24-g9f37358"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3295,11 +3290,11 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.3",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main'"
--- a/target/nextflow/io/publish/nextflow_schema.json
+++ b/target/nextflow/io/publish/nextflow_schema.json
@@ -67,10 +67,10 @@
                "output": {
                "type":
                "string",
-                "description": "Type: `file`, default: `$id.$key.output.output`. ",
-                "help_text": "Type: `file`, default: `$id.$key.output.output`. "
+                "description": "Type: `file`, default: `fastq`. ",
+                "help_text": "Type: `file`, default: `fastq`. "
            ,
-                "default":"$id.$key.output.output"
+                "default":"fastq"
            }
    

@@ -78,10 +78,10 @@
                "output_falco": {
                "type":
                "string",
-                "description": "Type: `file`, default: `$id.$key.output_falco.output_falco`. ",
-                "help_text": "Type: `file`, default: `$id.$key.output_falco.output_falco`. "
+                "description": "Type: `file`, default: `qc/fastqc`. ",
+                "help_text": "Type: `file`, default: `qc/fastqc`. "
            ,
-                "default":"$id.$key.output_falco.output_falco"
+                "default":"qc/fastqc"
            }
    

@@ -89,10 +89,10 @@
                "output_multiqc": {
                "type":
                "string",
-                "description": "Type: `file`, default: `$id.$key.output_multiqc.html`. ",
-                "help_text": "Type: `file`, default: `$id.$key.output_multiqc.html`. "
+                "description": "Type: `file`, default: `qc/multiqc_report.html`. ",
+                "help_text": "Type: `file`, default: `qc/multiqc_report.html`. "
            ,
-                "default":"$id.$key.output_multiqc.html"
+                "default":"qc/multiqc_report.html"
            }
    

@@ -100,10 +100,10 @@
                "output_run_information": {
                "type":
                "string",
-                "description": "Type: `file`, default: `$id.$key.output_run_information.csv`. ",
-                "help_text": "Type: `file`, default: `$id.$key.output_run_information.csv`. "
+                "description": "Type: `file`, default: `run_information.csv`. ",
+                "help_text": "Type: `file`, default: `run_information.csv`. "
            ,
-                "default":"$id.$key.output_run_information.csv"
+                "default":"run_information.csv"
            }
    

--- a/target/nextflow/io/untar/.config.vsh.yaml
+++ b/target/nextflow/io/untar/.config.vsh.yaml
@@ -155,10 +155,10 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/io/untar"
  executable: "target/nextflow/io/untar/main.nf"
-  viash_version: "0.9.3"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  viash_version: "0.9.4"
+  git_commit: "9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-22-g162497a"
+  git_tag: "v0.1.1-24-g9f37358"
 package_config:
  name: "demultiplex"
  version: "main"
@@ -167,11 +167,11 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/demultiplex/v2/"
      dest: "testData"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
+  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'\n"
--- a/target/nextflow/io/untar/main.nf
+++ b/target/nextflow/io/untar/main.nf
@@ -1,6 +1,6 @@
 // untar main
 // 
-// This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3231,10 +3226,10 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/io/untar",
-    "viash_version" : "0.9.3",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "viash_version" : "0.9.4",
+    "git_commit" : "9f37358ebfc77012c8c0dedd79a40e27b121c6c1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-22-g162497a"
+    "git_tag" : "v0.1.1-24-g9f37358"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3248,11 +3243,11 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.3",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main'"
--- a/target/nextflow/io/untar/nextflow_schema.json
+++ b/target/nextflow/io/untar/nextflow_schema.json
@@ -37,10 +37,10 @@
                "output": {
                "type":
                "string",
-                "description": "Type: `file`, required, default: `$id.$key.output.output`. Directory to write the contents of the ",
-                "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Directory to write the contents of the .tar file to."
+                "description": "Type: `file`, required, default: `$id.$key.output`. Directory to write the contents of the ",
+                "help_text": "Type: `file`, required, default: `$id.$key.output`. Directory to write the contents of the .tar file to."
            ,
-                "default":"$id.$key.output.output"
+                "default":"$id.$key.output"
            }
    

--- a/target/nextflow/runner/.config.vsh.yaml
+++ b/target/nextflow/runner/.config.vsh.yaml
@@ -194,10 +194,10 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/runner"
  executable: "target/nextflow/runner/main.nf"
-  viash_version: "0.9.3"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  viash_version: "0.9.4"
+  git_commit: "9f37358ebfc77012c8c0dedd79a40e27b121c6c1"
  git_remote: "https://github.com/viash-hub/demultiplex"
-  git_tag: "v0.1.1-22-g162497a"
+  git_tag: "v0.1.1-24-g9f37358"
  dependencies:
  - "target/nextflow/demultiplex"
  - "target/nextflow/io/publish"
@@ -209,11 +209,11 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/demultiplex/v2/"
      dest: "testData"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
-  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
+  - ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n\
    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
    )'\n"
--- a/target/nextflow/runner/main.nf
+++ b/target/nextflow/runner/main.nf
@@ -1,6 +1,6 @@
 // runner main
 // 
-// This wrapper script is auto-generated by viash 0.9.3 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3274,10 +3269,10 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/runner",
-    "viash_version" : "0.9.3",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "viash_version" : "0.9.4",
+    "git_commit" : "9f37358ebfc77012c8c0dedd79a40e27b121c6c1",
    "git_remote" : "https://github.com/viash-hub/demultiplex",
-    "git_tag" : "v0.1.1-22-g162497a"
+    "git_tag" : "v0.1.1-24-g9f37358"
  },
  "package_config" : {
    "name" : "demultiplex",
@@ -3291,11 +3286,11 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.3",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
-      ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
+      ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
      ".engines[.type == 'docker'].target_tag := 'main'"
--- a/target/nextflow/runner/nextflow_schema.json
+++ b/target/nextflow/runner/nextflow_schema.json
@@ -80,10 +80,10 @@
                "fastq_output": {
                "type":
                "string",
-                "description": "Type: `file`, default: `$id.$key.fastq_output.fastq_output`. ",
-                "help_text": "Type: `file`, default: `$id.$key.fastq_output.fastq_output`. "
+                "description": "Type: `file`, default: `fastq`. ",
+                "help_text": "Type: `file`, default: `fastq`. "
            ,
-                "default":"$id.$key.fastq_output.fastq_output"
+                "default":"fastq"
            }
    

@@ -91,10 +91,10 @@
                "falco_output": {
                "type":
                "string",
-                "description": "Type: `file`, default: `$id.$key.falco_output.falco_output`. ",
-                "help_text": "Type: `file`, default: `$id.$key.falco_output.falco_output`. "
+                "description": "Type: `file`, default: `qc/fastqc`. ",
+                "help_text": "Type: `file`, default: `qc/fastqc`. "
            ,
-                "default":"$id.$key.falco_output.falco_output"
+                "default":"qc/fastqc"
            }
    

@@ -102,10 +102,10 @@
                "multiqc_output": {
                "type":
                "string",
-                "description": "Type: `file`, default: `$id.$key.multiqc_output.html`. ",
-                "help_text": "Type: `file`, default: `$id.$key.multiqc_output.html`. "
+                "description": "Type: `file`, default: `qc/multiqc_report.html`. ",
+                "help_text": "Type: `file`, default: `qc/multiqc_report.html`. "
            ,
-                "default":"$id.$key.multiqc_output.html"
+                "default":"qc/multiqc_report.html"
            }