Build branch main with version main (1c2d4e9)

Build pipeline: viash-hub.craftbox.main-xsbs6

Source commit: 1c2d4e9054

Source message: Update readme and metadata (#11)

* update readme and metadata

* update github action

* apply changes

CHANGELOG.md

@@ -10,7 +10,9 @@
 
 * Add documentation to multiple components (PR #9).
 
-* Bump Viash to 0.9.3 (PR #9).
+* Bump Viash to 0.9.4 (PR #9, PR #11).
+
+* Update documentation and package metadata (PR #11).
 
 ## BUG FIXES
 

README.md

@@ -2,41 +2,126 @@
 
 # 🪡📦 craftbox
 
-[![ViashHub](https://img.shields.io/badge/ViashHub-craftbox-7a4baa.png)](https://web.viash-hub.com/packages/craftbox)
+[![ViashHub](https://img.shields.io/badge/ViashHub-craftbox-7a4baa.svg)](https://www.viash-hub.com/packages/craftbox)
-[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fcraftbox-blue.png)](https://github.com/viash-hub/craftbox)
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fcraftbox-blue.svg)](https://github.com/viash-hub/craftbox)
 [![GitHub
-License](https://img.shields.io/github/license/viash-hub/craftbox.png)](https://github.com/viash-hub/craftbox/blob/main/LICENSE)
+License](https://img.shields.io/github/license/viash-hub/craftbox.svg)](https://github.com/viash-hub/craftbox/blob/main/LICENSE)
 [![GitHub
-Issues](https://img.shields.io/github/issues/viash-hub/craftbox.png)](https://github.com/viash-hub/craftbox/issues)
+Issues](https://img.shields.io/github/issues/viash-hub/craftbox.svg)](https://github.com/viash-hub/craftbox/issues)
 [![Viash
-version](https://img.shields.io/badge/Viash-v0.9.0--RC7-blue)](https://viash.io)
+version](https://img.shields.io/badge/Viash-v0.9.4-blue.svg)](https://viash.io)
 
-A collection of custom-tailored scripts and applied tools.
+A collection of custom-tailored scripts and applied utilities built with
+Viash.
 
-## Objectives
+## Introduction
 
-- **Reusability**: Facilitating the use of components across various
+`craftbox` is a curated collection of custom scripts and utilities
-  projects and contexts.
+designed to tackle context-specific tasks.
-- **Reproducibility**: Ensuring that components are reproducible and can
+
-  be easily shared.
+Emphasizing the Viash principles, `craftbox` components aim for
-- **Best Practices**: Adhering to established standards in software
+**reusability**, **reproducibility**, and adherence to **best
-  development and bioinformatics.
+practices**. Key features generally include:
+
+- **Standalone & Nextflow Ready:** Components are built to run directly
+  via the command line or be smoothly integrated into Nextflow
+  workflows.
+- **Custom Implementations:** Contains scripts and tools developed for
+  particular tasks that may not be found in broader collections.
+- **High Quality Standards (promoted by Viash):**
+  - Clear documentation for components and their parameters.
+  - Full exposure of underlying script/tool arguments for fine-grained
+    control.
+  - Containerized (Docker) to ensure dependency management and a
+    consistent, reproducible runtime environment.
+  - Unit tested where applicable to ensure components function as
+    expected.
+
+## Example Usage
+
+Viash components in craftbox can be run in various ways:
+
+``` mermaid lang="mermaid
+flowchart TD
+    A[craftbox v0.2.0] --> B(Viash Hub Launch)
+    A --> C(Viash CLI)
+    A --> D(Nextflow CLI)
+    A --> E(Seqera Cloud)
+    A --> F(As a dependency)
+```
+
+### 1. Via the Viash Hub Launch interface
+
+You can run this component directly from the Viash Hub [Launch
+interface](https://www.viash-hub.com/launch?package=craftbox&version=v0.2.0&component=concat_rtext&runner=Executable).
+
+![](docs/viash-hub.png)
+
+### 2. Via the Viash CLI
+
+You can run this component directly from the command line using the
+Viash CLI.
+
+``` bash
+viash run vsh://craftbox@v0.2.0/concat_rtext -- --help
+
+viash run vsh://craftbox@v0.2.0/concat_rtext -- \
+  --input path/to/input.txt \
+  --input path/to/compressed.txt.gz \
+  --output path/to/output.txt
+```
+
+This will run the component with the specified input files and output
+the results to the specified output file.
+
+### 3. Via the Nextflow CLI or Seqera Cloud
+
+You can run this component as a Nextflow pipeline.
+
+``` bash
+nextflow run https://packages.viash-hub.com/vsh/craftbox \
+  -revision v0.2.0 \
+  -main-script target/nextflow/concat_rtext/main.nf \
+  -latest -resume \
+  -profile docker \
+  --input "path/to/input.txt;path/to/compressed.txt.gz" \
+  --output path/to/output.txt
+```
+
+**Note:** Make sure that the [Nextflow
+SCM](https://www.nextflow.io/docs/latest/git.html#git-configuration) is
+set up properly. You can do this by adding the following lines to your
+`~/.nextflow/scm` file:
+
+``` groovy
+providers.vsh.platform = 'gitlab'
+providers.vsh.server = 'https://packages.viash-hub.com'
+```
+
+**Tip:** This will also work with Seqera Cloud or other
+Nextflow-compatible platforms.
+
+### 4. As a dependency
+
+In your Viash config file (`config.vsh.yaml`), you can add this
+component as a dependency:
+
+``` yaml
+dependencies:
+  - name: concat_rtext
+    repository: vsh://craftbox@v0.2.0
+```
+
+**Tip:** See the [Viash
+documentation](https://viash.io/guide/nextflow_vdsl3/create-a-pipeline.html#pipeline-as-a-component)
+for more details on how to use Viash components as a dependency in your
+own Nextflow workflows.
 
 ## Contributing
 
-We encourage contributions from the community. To contribute:
+Contributions are welcome! We aim to build a comprehensive collection of
-
+high-quality bioinformatics components. If you’d like to contribute,
-1.  **Fork the Repository**: Start by forking this repository to your
+please follow these general steps:
-    account.
-2.  **Develop Your Component**: Create your Viash component, ensuring it
-    aligns with our best practices (detailed below).
-3.  **Submit a Pull Request**: After testing your component, submit a
-    pull request for review.
-
-## Contribution Guidelines
-
-The contribution guidelines describes which steps you should follow to
-contribute a component to this repository.
 
 1.  Find a component to contribute
 2.  Add config template
@@ -55,18 +140,3 @@ contribute a component to this repository.
 See the
 [CONTRIBUTING](https://github.com/viash-hub/craftbox/blob/main/CONTRIBUTING.md)
 file for more details.
-
-## Support and Community
-
-For support, questions, or to join our community:
-
-- **Issues**: Submit questions or issues via the [GitHub issue
-  tracker](https://github.com/viash-hub/craftbox/issues).
-- **Discussions**: Join our discussions via [GitHub
-  Discussions](https://github.com/viash-hub/craftbox/discussions).
-
-## License
-
-This repository is licensed under an MIT license. See the
-[LICENSE](https://github.com/viash-hub/craftbox/blob/main/LICENSE) file
-for details.

README.qmd

@@ -2,37 +2,106 @@
 format: gfm
 ---
 ```{r setup, include=FALSE}
-project <- yaml::read_yaml("_viash.yaml")
+package <- yaml::read_yaml("_viash.yaml")
-license <- paste0(project$links$repository, "/blob/main/LICENSE")
+license <- paste0(package$links$repository, "/blob/main/LICENSE")
-contributing <- paste0(project$links$repository, "/blob/main/CONTRIBUTING.md")
+contributing <- paste0(package$links$repository, "/blob/main/CONTRIBUTING.md")
+
+pkg <- package$name
+ver <- if (!is.null(package$version)) package$version else "v0.2.0"
+comp <- "concat_rtext"
 ```
-# 🪡📦 `r project$name`
+# 🪡📦 `r pkg`
 
-[![ViashHub](https://img.shields.io/badge/ViashHub-`r project$name`-7a4baa)](https://web.viash-hub.com/packages/`r project$name`) 
+[![ViashHub](https://img.shields.io/badge/ViashHub-`r pkg`-7a4baa.svg)](https://www.viash-hub.com/packages/`r pkg`) 
-[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2F`r project$name`-blue)](`r project$links$repository`) 
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2F`r pkg`-blue.svg)](`r package$links$repository`) 
-[![GitHub License](https://img.shields.io/github/license/viash-hub/`r project$name`)](`r license`) 
+[![GitHub License](https://img.shields.io/github/license/viash-hub/`r pkg`.svg)](`r license`) 
-[![GitHub Issues](https://img.shields.io/github/issues/viash-hub/`r project$name`)](`r project$links$issue_tracker`) 
+[![GitHub Issues](https://img.shields.io/github/issues/viash-hub/`r pkg`.svg)](`r package$links$issue_tracker`) 
-[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", project$viash_version)`-blue)](https://viash.io)
+[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", package$viash_version)`-blue.svg)](https://viash.io)
 
-`r project$description`
+`r package$summary`
 
-## Objectives
+## Introduction
 
-- **Reusability**: Facilitating the use of components across various projects and contexts.
+`r package$description`
-- **Reproducibility**: Ensuring that components are reproducible and can be easily shared.
+
-- **Best Practices**: Adhering to established standards in software development and bioinformatics.
+## Example Usage
+
+Viash components in `r pkg` can be run in various ways:
+
+```{r mmd, echo=FALSE, results='asis'}
+cat(
+  "```mermaid\n",
+  "flowchart TD\n",
+  "    A[", pkg, " ", ver, "] --> B(Viash Hub Launch)\n",
+  "    A --> C(Viash CLI)\n",
+  "    A --> D(Nextflow CLI)\n",
+  "    A --> E(Seqera Cloud)\n",
+  "    A --> F(As a dependency)\n",
+  "```\n",
+  sep = ""
+)
+```
+
+### 1. Via the Viash Hub Launch interface
+
+You can run this component directly from the Viash Hub [Launch interface](https://www.viash-hub.com/launch?package=`r pkg`&version=`r ver`&component=`r comp`&runner=Executable).
+
+![](docs/viash-hub.png)
+
+### 2. Via the Viash CLI
+
+You can run this component directly from the command line using the Viash CLI.
+
+```bash
+viash run vsh://`r pkg`@`r ver`/`r comp` -- --help
+
+viash run vsh://`r pkg`@`r ver`/`r comp` -- \
+  --input path/to/input.txt \
+  --input path/to/compressed.txt.gz \
+  --output path/to/output.txt
+```
+
+This will run the component with the specified input files and output the results to the specified output file.
+
+### 3. Via the Nextflow CLI or Seqera Cloud
+
+You can run this component as a Nextflow pipeline.
+
+```bash
+nextflow run https://packages.viash-hub.com/vsh/`r pkg` \
+  -revision `r ver` \
+  -main-script target/nextflow/`r comp`/main.nf \
+  -latest -resume \
+  -profile docker \
+  --input "path/to/input.txt;path/to/compressed.txt.gz" \
+  --output path/to/output.txt
+```
+
+**Note:** Make sure that the [Nextflow SCM](https://www.nextflow.io/docs/latest/git.html#git-configuration) is set up properly. You can do this by adding the following lines to your `~/.nextflow/scm` file:
+
+```groovy
+providers.vsh.platform = 'gitlab'
+providers.vsh.server = 'https://packages.viash-hub.com'
+```
+
+**Tip:** This will also work with Seqera Cloud or other Nextflow-compatible platforms.
+
+### 4. As a dependency
+
+In your Viash config file (`config.vsh.yaml`), you can add this component as a dependency:
+
+```yaml
+dependencies:
+  - name: `r comp`
+    repository: vsh://`r pkg`@`r ver`
+```
+
+**Tip:** See the [Viash documentation](https://viash.io/guide/nextflow_vdsl3/create-a-pipeline.html#pipeline-as-a-component) for more details on how to use Viash components as a dependency in your own Nextflow workflows.
 
 ## Contributing
 
-We encourage contributions from the community. To contribute:
+Contributions are welcome! We aim to build a comprehensive collection of high-quality bioinformatics components. If you'd like to contribute, please follow these general steps:
 
-1. **Fork the Repository**: Start by forking this repository to your account.
-2. **Develop Your Component**: Create your Viash component, ensuring it aligns with our best practices (detailed below).
-3. **Submit a Pull Request**: After testing your component, submit a pull request for review.
-
-## Contribution Guidelines
-
-The contribution guidelines describes which steps you should follow to contribute a component to this repository.
 
 ```{r echo=FALSE}
 lines <- readr::read_lines("CONTRIBUTING.md")
@@ -49,14 +118,3 @@ knitr::asis_output(
 ```
 
 See the [CONTRIBUTING](`r contributing`) file for more details.
-
-
-## Support and Community
-
-For support, questions, or to join our community:
-
-- **Issues**: Submit questions or issues via the [GitHub issue tracker](`r project$links$issue_tracker`).
-- **Discussions**: Join our discussions via [GitHub Discussions](`r project$links$repository`/discussions).
-
-## License
-This repository is licensed under an MIT license. See the [LICENSE](`r license`) file for details.

_viash.yaml

@@ -1,13 +1,25 @@
 name: craftbox
+summary: |
+  A collection of custom-tailored scripts and applied utilities built with Viash.
 description: |
-  A collection of custom-tailored scripts and applied tools.
+  `craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.
+
+  Emphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:
+
+  * **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.
+  * **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.
+  * **High Quality Standards (promoted by Viash):**
+      * Clear documentation for components and their parameters.
+      * Full exposure of underlying script/tool arguments for fine-grained control.
+      * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.
+      * Unit tested where applicable to ensure components function as expected.
+keywords: [scripts, custom, implementations, utilities]
 license: MIT
-keywords: [scripts, custom, implementations]
 links:
   issue_tracker: https://github.com/viash-hub/craftbox/issues
   repository: https://github.com/viash-hub/craftbox
 
-viash_version: 0.9.3
+viash_version: 0.9.4
 
 config_mods: |
   .requirements.commands := ['ps']

target/executable/concat_text/.config.vsh.yaml

@@ -174,16 +174,29 @@ build_info:
   engine: "docker|native"
   output: "target/executable/concat_text"
   executable: "target/executable/concat_text/concat_text"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
-  git_commit: "9ca16ea58d5f010e31714265802c016280594624"
+  git_commit: "1c2d4e90541ed3c2e04a2633db86413b2548ab10"
   git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-5-g9ca16ea"
+  git_tag: "v0.1.0-6-g1c2d4e9"
 package_config:
   name: "craftbox"
   version: "main"
-  description: "A collection of custom-tailored scripts and applied tools.\n"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
   info: null
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:
@@ -195,6 +208,7 @@ package_config:
   - "scripts"
   - "custom"
   - "implementations"
+  - "utilities"
   license: "MIT"
   organization: "vsh"
   links:

target/executable/concat_text/concat_text

@@ -2,7 +2,7 @@
 
 # concat_text 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.
 # 
@@ -453,9 +453,9 @@ RUN apk add --no-cache bash procps file
 
 LABEL org.opencontainers.image.authors="Toni Verbeiren, Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component concat_text"
-LABEL org.opencontainers.image.created="2025-05-02T09:33:23Z"
+LABEL org.opencontainers.image.created="2025-05-07T13:45:23Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="9ca16ea58d5f010e31714265802c016280594624"
+LABEL org.opencontainers.image.revision="1c2d4e90541ed3c2e04a2633db86413b2548ab10"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/csv2fasta/.config.vsh.yaml

@@ -256,16 +256,29 @@ build_info:
   engine: "docker|native"
   output: "target/executable/csv2fasta"
   executable: "target/executable/csv2fasta/csv2fasta"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
-  git_commit: "9ca16ea58d5f010e31714265802c016280594624"
+  git_commit: "1c2d4e90541ed3c2e04a2633db86413b2548ab10"
   git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-5-g9ca16ea"
+  git_tag: "v0.1.0-6-g1c2d4e9"
 package_config:
   name: "craftbox"
   version: "main"
-  description: "A collection of custom-tailored scripts and applied tools.\n"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
   info: null
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:
@@ -277,6 +290,7 @@ package_config:
   - "scripts"
   - "custom"
   - "implementations"
+  - "utilities"
   license: "MIT"
   organization: "vsh"
   links:

target/executable/csv2fasta/csv2fasta

@@ -2,7 +2,7 @@
 
 # csv2fasta 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.
 # 
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component csv2fasta"
-LABEL org.opencontainers.image.created="2025-05-02T09:33:24Z"
+LABEL org.opencontainers.image.created="2025-05-07T13:45:23Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="9ca16ea58d5f010e31714265802c016280594624"
+LABEL org.opencontainers.image.revision="1c2d4e90541ed3c2e04a2633db86413b2548ab10"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/move_files_to_directory/.config.vsh.yaml

@@ -145,16 +145,29 @@ build_info:
   engine: "docker|native"
   output: "target/executable/move_files_to_directory"
   executable: "target/executable/move_files_to_directory/move_files_to_directory"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
-  git_commit: "9ca16ea58d5f010e31714265802c016280594624"
+  git_commit: "1c2d4e90541ed3c2e04a2633db86413b2548ab10"
   git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-5-g9ca16ea"
+  git_tag: "v0.1.0-6-g1c2d4e9"
 package_config:
   name: "craftbox"
   version: "main"
-  description: "A collection of custom-tailored scripts and applied tools.\n"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
   info: null
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:
@@ -166,6 +179,7 @@ package_config:
   - "scripts"
   - "custom"
   - "implementations"
+  - "utilities"
   license: "MIT"
   organization: "vsh"
   links:

target/executable/move_files_to_directory/move_files_to_directory

@@ -2,7 +2,7 @@
 
 # move_files_to_directory 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 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component move_files_to_directory"
-LABEL org.opencontainers.image.created="2025-05-02T09:33:23Z"
+LABEL org.opencontainers.image.created="2025-05-07T13:45:23Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="9ca16ea58d5f010e31714265802c016280594624"
+LABEL org.opencontainers.image.revision="1c2d4e90541ed3c2e04a2633db86413b2548ab10"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/sync_resources/.config.vsh.yaml

@@ -196,16 +196,29 @@ build_info:
   engine: "docker|native"
   output: "target/executable/sync_resources"
   executable: "target/executable/sync_resources/sync_resources"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
-  git_commit: "9ca16ea58d5f010e31714265802c016280594624"
+  git_commit: "1c2d4e90541ed3c2e04a2633db86413b2548ab10"
   git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-5-g9ca16ea"
+  git_tag: "v0.1.0-6-g1c2d4e9"
 package_config:
   name: "craftbox"
   version: "main"
-  description: "A collection of custom-tailored scripts and applied tools.\n"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
   info: null
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:
@@ -217,6 +230,7 @@ package_config:
   - "scripts"
   - "custom"
   - "implementations"
+  - "utilities"
   license: "MIT"
   organization: "vsh"
   links:

target/executable/sync_resources/sync_resources

@@ -2,7 +2,7 @@
 
 # sync_resources 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.
 # 
@@ -455,9 +455,9 @@ RUN rclone config create s3 s3 anonymous=true
 RUN rclone config create gs gcs anonymous=true
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component sync_resources"
-LABEL org.opencontainers.image.created="2025-05-02T09:33:24Z"
+LABEL org.opencontainers.image.created="2025-05-07T13:45:23Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="9ca16ea58d5f010e31714265802c016280594624"
+LABEL org.opencontainers.image.revision="1c2d4e90541ed3c2e04a2633db86413b2548ab10"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -181,16 +181,29 @@ build_info:
   engine: "docker|native"
   output: "target/executable/untar"
   executable: "target/executable/untar/untar"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
-  git_commit: "9ca16ea58d5f010e31714265802c016280594624"
+  git_commit: "1c2d4e90541ed3c2e04a2633db86413b2548ab10"
   git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-5-g9ca16ea"
+  git_tag: "v0.1.0-6-g1c2d4e9"
 package_config:
   name: "craftbox"
   version: "main"
-  description: "A collection of custom-tailored scripts and applied tools.\n"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
   info: null
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:
@@ -202,6 +215,7 @@ package_config:
   - "scripts"
   - "custom"
   - "implementations"
+  - "utilities"
   license: "MIT"
   organization: "vsh"
   links:

target/executable/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.
 # 
@@ -455,9 +455,9 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component untar"
-LABEL org.opencontainers.image.created="2025-05-02T09:33:23Z"
+LABEL org.opencontainers.image.created="2025-05-07T13:45:23Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="9ca16ea58d5f010e31714265802c016280594624"
+LABEL org.opencontainers.image.revision="1c2d4e90541ed3c2e04a2633db86413b2548ab10"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/nextflow/concat_text/.config.vsh.yaml

@@ -174,16 +174,29 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/concat_text"
   executable: "target/nextflow/concat_text/main.nf"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
-  git_commit: "9ca16ea58d5f010e31714265802c016280594624"
+  git_commit: "1c2d4e90541ed3c2e04a2633db86413b2548ab10"
   git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-5-g9ca16ea"
+  git_tag: "v0.1.0-6-g1c2d4e9"
 package_config:
   name: "craftbox"
   version: "main"
-  description: "A collection of custom-tailored scripts and applied tools.\n"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
   info: null
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:
@@ -195,6 +208,7 @@ package_config:
   - "scripts"
   - "custom"
   - "implementations"
+  - "utilities"
   license: "MIT"
   organization: "vsh"
   links:

target/nextflow/concat_text/main.nf

@@ -1,6 +1,6 @@
 // concat_text 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.
 // 
@@ -86,64 +86,56 @@ 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) {
@@ -155,10 +147,13 @@ 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
@@ -3266,16 +3261,17 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/concat_text",
-    "viash_version" : "0.9.3",
+    "viash_version" : "0.9.4",
-    "git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
+    "git_commit" : "1c2d4e90541ed3c2e04a2633db86413b2548ab10",
     "git_remote" : "https://github.com/viash-hub/craftbox",
-    "git_tag" : "v0.1.0-5-g9ca16ea"
+    "git_tag" : "v0.1.0-6-g1c2d4e9"
   },
   "package_config" : {
     "name" : "craftbox",
     "version" : "main",
-    "description" : "A collection of custom-tailored scripts and applied tools.\n",
+    "summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
-    "viash_version" : "0.9.3",
+    "description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear documentation for components and their parameters.\n    * Full exposure of underlying script/tool arguments for fine-grained control.\n    * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n    * Unit tested where applicable to ensure components function as expected.\n",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3287,7 +3283,8 @@ meta = [
     "keywords" : [
       "scripts",
       "custom",
-      "implementations"
+      "implementations",
+      "utilities"
     ],
     "license" : "MIT",
     "organization" : "vsh",

target/nextflow/csv2fasta/.config.vsh.yaml

@@ -256,16 +256,29 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/csv2fasta"
   executable: "target/nextflow/csv2fasta/main.nf"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
-  git_commit: "9ca16ea58d5f010e31714265802c016280594624"
+  git_commit: "1c2d4e90541ed3c2e04a2633db86413b2548ab10"
   git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-5-g9ca16ea"
+  git_tag: "v0.1.0-6-g1c2d4e9"
 package_config:
   name: "craftbox"
   version: "main"
-  description: "A collection of custom-tailored scripts and applied tools.\n"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
   info: null
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:
@@ -277,6 +290,7 @@ package_config:
   - "scripts"
   - "custom"
   - "implementations"
+  - "utilities"
   license: "MIT"
   organization: "vsh"
   links:

target/nextflow/csv2fasta/main.nf

@@ -1,6 +1,6 @@
 // csv2fasta 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.
 // 
@@ -86,64 +86,56 @@ 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) {
@@ -155,10 +147,13 @@ 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
@@ -3356,16 +3351,17 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/csv2fasta",
-    "viash_version" : "0.9.3",
+    "viash_version" : "0.9.4",
-    "git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
+    "git_commit" : "1c2d4e90541ed3c2e04a2633db86413b2548ab10",
     "git_remote" : "https://github.com/viash-hub/craftbox",
-    "git_tag" : "v0.1.0-5-g9ca16ea"
+    "git_tag" : "v0.1.0-6-g1c2d4e9"
   },
   "package_config" : {
     "name" : "craftbox",
     "version" : "main",
-    "description" : "A collection of custom-tailored scripts and applied tools.\n",
+    "summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
-    "viash_version" : "0.9.3",
+    "description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear documentation for components and their parameters.\n    * Full exposure of underlying script/tool arguments for fine-grained control.\n    * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n    * Unit tested where applicable to ensure components function as expected.\n",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3377,7 +3373,8 @@ meta = [
     "keywords" : [
       "scripts",
       "custom",
-      "implementations"
+      "implementations",
+      "utilities"
     ],
     "license" : "MIT",
     "organization" : "vsh",

target/nextflow/move_files_to_directory/.config.vsh.yaml

@@ -145,16 +145,29 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/move_files_to_directory"
   executable: "target/nextflow/move_files_to_directory/main.nf"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
-  git_commit: "9ca16ea58d5f010e31714265802c016280594624"
+  git_commit: "1c2d4e90541ed3c2e04a2633db86413b2548ab10"
   git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-5-g9ca16ea"
+  git_tag: "v0.1.0-6-g1c2d4e9"
 package_config:
   name: "craftbox"
   version: "main"
-  description: "A collection of custom-tailored scripts and applied tools.\n"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
   info: null
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:
@@ -166,6 +179,7 @@ package_config:
   - "scripts"
   - "custom"
   - "implementations"
+  - "utilities"
   license: "MIT"
   organization: "vsh"
   links:

target/nextflow/move_files_to_directory/main.nf

@@ -1,6 +1,6 @@
 // move_files_to_directory 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.
 // 
@@ -85,64 +85,56 @@ 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) {
@@ -154,10 +146,13 @@ 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
@@ -3223,16 +3218,17 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/move_files_to_directory",
-    "viash_version" : "0.9.3",
+    "viash_version" : "0.9.4",
-    "git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
+    "git_commit" : "1c2d4e90541ed3c2e04a2633db86413b2548ab10",
     "git_remote" : "https://github.com/viash-hub/craftbox",
-    "git_tag" : "v0.1.0-5-g9ca16ea"
+    "git_tag" : "v0.1.0-6-g1c2d4e9"
   },
   "package_config" : {
     "name" : "craftbox",
     "version" : "main",
-    "description" : "A collection of custom-tailored scripts and applied tools.\n",
+    "summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
-    "viash_version" : "0.9.3",
+    "description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear documentation for components and their parameters.\n    * Full exposure of underlying script/tool arguments for fine-grained control.\n    * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n    * Unit tested where applicable to ensure components function as expected.\n",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3244,7 +3240,8 @@ meta = [
     "keywords" : [
       "scripts",
       "custom",
-      "implementations"
+      "implementations",
+      "utilities"
     ],
     "license" : "MIT",
     "organization" : "vsh",

target/nextflow/sync_resources/.config.vsh.yaml

@@ -196,16 +196,29 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/sync_resources"
   executable: "target/nextflow/sync_resources/main.nf"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
-  git_commit: "9ca16ea58d5f010e31714265802c016280594624"
+  git_commit: "1c2d4e90541ed3c2e04a2633db86413b2548ab10"
   git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-5-g9ca16ea"
+  git_tag: "v0.1.0-6-g1c2d4e9"
 package_config:
   name: "craftbox"
   version: "main"
-  description: "A collection of custom-tailored scripts and applied tools.\n"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
   info: null
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:
@@ -217,6 +230,7 @@ package_config:
   - "scripts"
   - "custom"
   - "implementations"
+  - "utilities"
   license: "MIT"
   organization: "vsh"
   links:

target/nextflow/sync_resources/main.nf

@@ -1,6 +1,6 @@
 // sync_resources 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.
 // 
@@ -86,64 +86,56 @@ 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) {
@@ -155,10 +147,13 @@ 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
@@ -3298,16 +3293,17 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/sync_resources",
-    "viash_version" : "0.9.3",
+    "viash_version" : "0.9.4",
-    "git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
+    "git_commit" : "1c2d4e90541ed3c2e04a2633db86413b2548ab10",
     "git_remote" : "https://github.com/viash-hub/craftbox",
-    "git_tag" : "v0.1.0-5-g9ca16ea"
+    "git_tag" : "v0.1.0-6-g1c2d4e9"
   },
   "package_config" : {
     "name" : "craftbox",
     "version" : "main",
-    "description" : "A collection of custom-tailored scripts and applied tools.\n",
+    "summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
-    "viash_version" : "0.9.3",
+    "description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear documentation for components and their parameters.\n    * Full exposure of underlying script/tool arguments for fine-grained control.\n    * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n    * Unit tested where applicable to ensure components function as expected.\n",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3319,7 +3315,8 @@ meta = [
     "keywords" : [
       "scripts",
       "custom",
-      "implementations"
+      "implementations",
+      "utilities"
     ],
     "license" : "MIT",
     "organization" : "vsh",

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

@@ -181,16 +181,29 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/untar"
   executable: "target/nextflow/untar/main.nf"
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
-  git_commit: "9ca16ea58d5f010e31714265802c016280594624"
+  git_commit: "1c2d4e90541ed3c2e04a2633db86413b2548ab10"
   git_remote: "https://github.com/viash-hub/craftbox"
-  git_tag: "v0.1.0-5-g9ca16ea"
+  git_tag: "v0.1.0-6-g1c2d4e9"
 package_config:
   name: "craftbox"
   version: "main"
-  description: "A collection of custom-tailored scripts and applied tools.\n"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
   info: null
-  viash_version: "0.9.3"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:
@@ -202,6 +215,7 @@ package_config:
   - "scripts"
   - "custom"
   - "implementations"
+  - "utilities"
   license: "MIT"
   organization: "vsh"
   links:

target/nextflow/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.
 // 
@@ -86,64 +86,56 @@ 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) {
@@ -155,10 +147,13 @@ 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
@@ -3277,16 +3272,17 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/untar",
-    "viash_version" : "0.9.3",
+    "viash_version" : "0.9.4",
-    "git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
+    "git_commit" : "1c2d4e90541ed3c2e04a2633db86413b2548ab10",
     "git_remote" : "https://github.com/viash-hub/craftbox",
-    "git_tag" : "v0.1.0-5-g9ca16ea"
+    "git_tag" : "v0.1.0-6-g1c2d4e9"
   },
   "package_config" : {
     "name" : "craftbox",
     "version" : "main",
-    "description" : "A collection of custom-tailored scripts and applied tools.\n",
+    "summary" : "A collection of custom-tailored scripts and applied utilities built with Viash.\n",
-    "viash_version" : "0.9.3",
+    "description" : "`craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.\n* **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear documentation for components and their parameters.\n    * Full exposure of underlying script/tool arguments for fine-grained control.\n    * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.\n    * Unit tested where applicable to ensure components function as expected.\n",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3298,7 +3294,8 @@ meta = [
     "keywords" : [
       "scripts",
       "custom",
-      "implementations"
+      "implementations",
+      "utilities"
     ],
     "license" : "MIT",
     "organization" : "vsh",