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)

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
 

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 \

_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")'

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"
+  viash_version: "0.9.4"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  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"

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

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"
+  viash_version: "0.9.4"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  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"

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

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"
+  viash_version: "0.9.4"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  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"

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

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"
+  viash_version: "0.9.4"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  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"

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) {
+  } else if (par.type == "float") {
-      value = value.doubleValue()
+    // 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) {
+    if (value !instanceof Boolean) {
-      def valueLower = value.toLowerCase()
+      try {
-      if (valueLower == "true") {
+        value = value as Boolean
-        value = true
+      } catch (Exception e) {
-      } else if (valueLower == "false") {
+        expectedClass = "Boolean"
-        value = false
       }
     }
-    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) {
+    if (value !instanceof String) {
-      value = value.toString()
+      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",
+    "viash_version" : "0.9.4",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "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'"

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: `\";\"`. ",
+                "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_*.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: `\";\"`. ",
+                "description": "Type: List of `file`, default: `$id.$key.output_reverse_*`, multiple_sep: `\";\"`. ",
-                "help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*.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: `\";\"`. ",
+                "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_*.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_*"
             }
     
 

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"
+  viash_version: "0.9.4"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  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"

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) {
+  } else if (par.type == "float") {
-      value = value.doubleValue()
+    // 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) {
+    if (value !instanceof Boolean) {
-      def valueLower = value.toLowerCase()
+      try {
-      if (valueLower == "true") {
+        value = value as Boolean
-        value = true
+      } catch (Exception e) {
-      } else if (valueLower == "false") {
+        expectedClass = "Boolean"
-        value = false
       }
     }
-    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) {
+    if (value !instanceof String) {
-      value = value.toString()
+      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",
+    "viash_version" : "0.9.4",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "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'"

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: `\";\"`. ",
+                "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_*.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: `\";\"`. ",
+                "description": "Type: List of `file`, default: `$id.$key.fastq_reverse_*`, multiple_sep: `\";\"`. ",
-                "help_text": "Type: List of `file`, default: `$id.$key.fastq_reverse_*.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_*"
             }
     
 

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"
+  viash_version: "0.9.4"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  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"

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) {
+  } else if (par.type == "float") {
-      value = value.doubleValue()
+    // 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) {
+    if (value !instanceof Boolean) {
-      def valueLower = value.toLowerCase()
+      try {
-      if (valueLower == "true") {
+        value = value as Boolean
-        value = true
+      } catch (Exception e) {
-      } else if (valueLower == "false") {
+        expectedClass = "Boolean"
-        value = false
       }
     }
-    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) {
+    if (value !instanceof String) {
-      value = value.toString()
+      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",
+    "viash_version" : "0.9.4",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "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'"

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",
+                "description": "Type: `file`, default: `$id/fastq`. Directory to write fastq data to",
-                "help_text": "Type: `file`, default: `$id.$key.output.output`. Directory to write fastq data to"
+                "help_text": "Type: `file`, default: `$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",
+                "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.$key.output_falco_*.output_falco_*`, multiple_sep: `\";\"`. Directory to write falco output to"
+                "help_text": "Type: List of `file`, default: `$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",
+                "description": "Type: `file`, default: `$id/qc/multiqc_report.html`. Directory to write falco output to",
-                "help_text": "Type: `file`, default: `$id.$key.output_multiqc.html`. Directory to write falco output to"
+                "help_text": "Type: `file`, default: `$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`. ",
+                "description": "Type: `file`, required, default: `$id/run_information.csv`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.output_run_information.csv`. "
+                "help_text": "Type: `file`, required, default: `$id/run_information.csv`. "
             ,
-                "default":"$id.$key.output_run_information.csv"
+                "default":"$id/run_information.csv"
             }
     
 

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"
+  viash_version: "0.9.4"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  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"

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) {
+  } else if (par.type == "float") {
-      value = value.doubleValue()
+    // 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) {
+    if (value !instanceof Boolean) {
-      def valueLower = value.toLowerCase()
+      try {
-      if (valueLower == "true") {
+        value = value as Boolean
-        value = true
+      } catch (Exception e) {
-      } else if (valueLower == "false") {
+        expectedClass = "Boolean"
-        value = false
       }
     }
-    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) {
+    if (value !instanceof String) {
-      value = value.toString()
+      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",
+    "viash_version" : "0.9.4",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "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'"

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`. ",
+                "description": "Type: `file`, required, default: `$id.$key.output_run_summary`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.output_run_summary.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`. ",
+                "description": "Type: `file`, required, default: `$id.$key.output_index_summary`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.output_index_summary.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"
             }
     
 

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"
+  viash_version: "0.9.4"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  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"

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) {
+  } else if (par.type == "float") {
-      value = value.doubleValue()
+    // 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) {
+    if (value !instanceof Boolean) {
-      def valueLower = value.toLowerCase()
+      try {
-      if (valueLower == "true") {
+        value = value as Boolean
-        value = true
+      } catch (Exception e) {
-      } else if (valueLower == "false") {
+        expectedClass = "Boolean"
-        value = false
       }
     }
-    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) {
+    if (value !instanceof String) {
-      value = value.toString()
+      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",
+    "viash_version" : "0.9.4",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "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'"

target/nextflow/io/publish/nextflow_schema.json

@@ -67,10 +67,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output.output`. ",
+                "description": "Type: `file`, default: `fastq`. ",
-                "help_text": "Type: `file`, default: `$id.$key.output.output`. "
+                "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`. ",
+                "description": "Type: `file`, default: `qc/fastqc`. ",
-                "help_text": "Type: `file`, default: `$id.$key.output_falco.output_falco`. "
+                "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`. ",
+                "description": "Type: `file`, default: `qc/multiqc_report.html`. ",
-                "help_text": "Type: `file`, default: `$id.$key.output_multiqc.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`. ",
+                "description": "Type: `file`, default: `run_information.csv`. ",
-                "help_text": "Type: `file`, default: `$id.$key.output_run_information.csv`. "
+                "help_text": "Type: `file`, default: `run_information.csv`. "
             ,
-                "default":"$id.$key.output_run_information.csv"
+                "default":"run_information.csv"
             }
     
 

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"
+  viash_version: "0.9.4"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  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"

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) {
+  } else if (par.type == "float") {
-      value = value.doubleValue()
+    // 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) {
+    if (value !instanceof Boolean) {
-      def valueLower = value.toLowerCase()
+      try {
-      if (valueLower == "true") {
+        value = value as Boolean
-        value = true
+      } catch (Exception e) {
-      } else if (valueLower == "false") {
+        expectedClass = "Boolean"
-        value = false
       }
     }
-    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) {
+    if (value !instanceof String) {
-      value = value.toString()
+      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",
+    "viash_version" : "0.9.4",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "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'"

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 ",
+                "description": "Type: `file`, required, default: `$id.$key.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."
+                "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"
             }
     
 

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"
+  viash_version: "0.9.4"
-  git_commit: "162497ab73faf321d5166fe34cd1f6976b14dcb0"
+  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"

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) {
+  } else if (par.type == "float") {
-      value = value.doubleValue()
+    // 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) {
+    if (value !instanceof Boolean) {
-      def valueLower = value.toLowerCase()
+      try {
-      if (valueLower == "true") {
+        value = value as Boolean
-        value = true
+      } catch (Exception e) {
-      } else if (valueLower == "false") {
+        expectedClass = "Boolean"
-        value = false
       }
     }
-    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) {
+    if (value !instanceof String) {
-      value = value.toString()
+      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",
+    "viash_version" : "0.9.4",
-    "git_commit" : "162497ab73faf321d5166fe34cd1f6976b14dcb0",
+    "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'"

target/nextflow/runner/nextflow_schema.json

@@ -80,10 +80,10 @@
                 "fastq_output": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.fastq_output.fastq_output`. ",
+                "description": "Type: `file`, default: `fastq`. ",
-                "help_text": "Type: `file`, default: `$id.$key.fastq_output.fastq_output`. "
+                "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`. ",
+                "description": "Type: `file`, default: `qc/fastqc`. ",
-                "help_text": "Type: `file`, default: `$id.$key.falco_output.falco_output`. "
+                "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`. ",
+                "description": "Type: `file`, default: `qc/multiqc_report.html`. ",
-                "help_text": "Type: `file`, default: `$id.$key.multiqc_output.html`. "
+                "help_text": "Type: `file`, default: `qc/multiqc_report.html`. "
             ,
-                "default":"$id.$key.multiqc_output.html"
+                "default":"qc/multiqc_report.html"
             }