vsh/craftbox
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Build branch main with version main (1c2d4e9)

Browse Source 
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
This commit is contained in:
CI
2025-05-07 13:51:35 +00:00
parent 1a32cb3ec3
commit 8ac9838721
25 changed files with 620 additions and 353 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
CHANGELOG.md
View File

@@ -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

152
README.md
View File

@@ -2,41 +2,126 @@
# 🪡📦 craftbox
[![ViashHub](https://img.shields.io/badge/ViashHub-craftbox-7a4baa.png)](https://web.viash-hub.com/packages/craftbox)
[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fcraftbox-blue.png)](https://github.com/viash-hub/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.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
projects and contexts.
- **Reproducibility**: Ensuring that components are reproducible and can
be easily shared.
- **Best Practices**: Adhering to established standards in software
development and bioinformatics.
`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.
## 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:
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.
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. 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.

124
README.qmd
View File

@@ -2,37 +2,106 @@
format: gfm
---
```{r setup, include=FALSE}
project <- yaml::read_yaml("_viash.yaml")
license <- paste0(project$links$repository, "/blob/main/LICENSE")
contributing <- paste0(project$links$repository, "/blob/main/CONTRIBUTING.md")
package <- yaml::read_yaml("_viash.yaml")
license <- paste0(package$links$repository, "/blob/main/LICENSE")
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`)
[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2F`r project$name`-blue)](`r project$links$repository`)
[![GitHub License](https://img.shields.io/github/license/viash-hub/`r project$name`)](`r license`)
[![GitHub Issues](https://img.shields.io/github/issues/viash-hub/`r project$name`)](`r project$links$issue_tracker`)
[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", project$viash_version)`-blue)](https://viash.io)
[![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 pkg`-blue.svg)](`r package$links$repository`)
[![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 pkg`.svg)](`r package$links$issue_tracker`)
[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", package$viash_version)`-blue.svg)](https://viash.io)
`r project$description`
`r package$summary`
## Objectives
## Introduction
- **Reusability**: Facilitating the use of components across various projects and contexts.
- **Reproducibility**: Ensuring that components are reproducible and can be easily shared.
- **Best Practices**: Adhering to established standards in software development and bioinformatics.
`r package$description`
## 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.

18
_viash.yaml
View File

@@ -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']

BIN
docs/viash-hub.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 148 KiB

24
target/executable/concat_text/.config.vsh.yaml
View File

@@ -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"
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
viash_version: "0.9.4"
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:

6
target/executable/concat_text/concat_text
View File

@@ -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

24
target/executable/csv2fasta/.config.vsh.yaml
View File

@@ -256,16 +256,29 @@ build_info:
engine: "docker|native"
output: "target/executable/csv2fasta"
executable: "target/executable/csv2fasta/csv2fasta"
viash_version: "0.9.3"
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
viash_version: "0.9.4"
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:

6
target/executable/csv2fasta/csv2fasta
View File

@@ -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

24
target/executable/move_files_to_directory/.config.vsh.yaml
View File

@@ -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"
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
viash_version: "0.9.4"
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:

6
target/executable/move_files_to_directory/move_files_to_directory
View File

@@ -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

24
target/executable/sync_resources/.config.vsh.yaml
View File

@@ -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"
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
viash_version: "0.9.4"
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:

6
target/executable/sync_resources/sync_resources
View File

@@ -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

24
target/executable/untar/.config.vsh.yaml
View File

@@ -181,16 +181,29 @@ build_info:
engine: "docker|native"
output: "target/executable/untar"
executable: "target/executable/untar/untar"
viash_version: "0.9.3"
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
viash_version: "0.9.4"
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:

6
target/executable/untar/untar
View File

@@ -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

24
target/nextflow/concat_text/.config.vsh.yaml
View File

@@ -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"
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
viash_version: "0.9.4"
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:

81
target/nextflow/concat_text/main.nf
View File

@@ -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) {
value = value.doubleValue()
} else if (par.type == "float") {
// cast to float if need be
if (value !instanceof Float) {
try {
value = value as Float
} catch (NumberFormatException e) {
expectedClass = "Float"
}
}
if (value instanceof Float) {
value = value.toDouble()
}
expectedClass = value instanceof Double ? null : "Double"
} else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
// cast to boolean if need be
if (value instanceof String) {
def valueLower = value.toLowerCase()
if (valueLower == "true") {
value = true
} else if (valueLower == "false") {
value = false
if (value !instanceof Boolean) {
try {
value = value as Boolean
} catch (Exception e) {
expectedClass = "Boolean"
}
}
expectedClass = value instanceof Boolean ? null : "Boolean"
} else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
// cast to path if need be
if (value instanceof String) {
@@ -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) {
value = value.toString()
if (value !instanceof String) {
try {
value = value as String
} catch (Exception e) {
expectedClass = "String"
}
}
expectedClass = value instanceof String ? null : "String"
} else {
// didn't find a match for par.type
expectedClass = par.type
@@ -3266,16 +3261,17 @@ meta = [
"runner" : "nextflow",
"engine" : "docker|native",
"output" : "target/nextflow/concat_text",
"viash_version" : "0.9.3",
"git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
"viash_version" : "0.9.4",
"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",
"viash_version" : "0.9.3",
"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",
"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",

24
target/nextflow/csv2fasta/.config.vsh.yaml
View File

@@ -256,16 +256,29 @@ build_info:
engine: "docker|native"
output: "target/nextflow/csv2fasta"
executable: "target/nextflow/csv2fasta/main.nf"
viash_version: "0.9.3"
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
viash_version: "0.9.4"
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:

81
target/nextflow/csv2fasta/main.nf
View File

@@ -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) {
value = value.doubleValue()
} else if (par.type == "float") {
// cast to float if need be
if (value !instanceof Float) {
try {
value = value as Float
} catch (NumberFormatException e) {
expectedClass = "Float"
}
}
if (value instanceof Float) {
value = value.toDouble()
}
expectedClass = value instanceof Double ? null : "Double"
} else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
// cast to boolean if need be
if (value instanceof String) {
def valueLower = value.toLowerCase()
if (valueLower == "true") {
value = true
} else if (valueLower == "false") {
value = false
if (value !instanceof Boolean) {
try {
value = value as Boolean
} catch (Exception e) {
expectedClass = "Boolean"
}
}
expectedClass = value instanceof Boolean ? null : "Boolean"
} else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
// cast to path if need be
if (value instanceof String) {
@@ -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) {
value = value.toString()
if (value !instanceof String) {
try {
value = value as String
} catch (Exception e) {
expectedClass = "String"
}
}
expectedClass = value instanceof String ? null : "String"
} else {
// didn't find a match for par.type
expectedClass = par.type
@@ -3356,16 +3351,17 @@ meta = [
"runner" : "nextflow",
"engine" : "docker|native",
"output" : "target/nextflow/csv2fasta",
"viash_version" : "0.9.3",
"git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
"viash_version" : "0.9.4",
"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",
"viash_version" : "0.9.3",
"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",
"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",

24
target/nextflow/move_files_to_directory/.config.vsh.yaml
View File

@@ -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"
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
viash_version: "0.9.4"
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:

81
target/nextflow/move_files_to_directory/main.nf
View File

@@ -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) {
value = value.doubleValue()
} else if (par.type == "float") {
// cast to float if need be
if (value !instanceof Float) {
try {
value = value as Float
} catch (NumberFormatException e) {
expectedClass = "Float"
}
}
if (value instanceof Float) {
value = value.toDouble()
}
expectedClass = value instanceof Double ? null : "Double"
} else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
// cast to boolean if need be
if (value instanceof String) {
def valueLower = value.toLowerCase()
if (valueLower == "true") {
value = true
} else if (valueLower == "false") {
value = false
if (value !instanceof Boolean) {
try {
value = value as Boolean
} catch (Exception e) {
expectedClass = "Boolean"
}
}
expectedClass = value instanceof Boolean ? null : "Boolean"
} else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
// cast to path if need be
if (value instanceof String) {
@@ -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) {
value = value.toString()
if (value !instanceof String) {
try {
value = value as String
} catch (Exception e) {
expectedClass = "String"
}
}
expectedClass = value instanceof String ? null : "String"
} else {
// didn't find a match for par.type
expectedClass = par.type
@@ -3223,16 +3218,17 @@ meta = [
"runner" : "nextflow",
"engine" : "docker|native",
"output" : "target/nextflow/move_files_to_directory",
"viash_version" : "0.9.3",
"git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
"viash_version" : "0.9.4",
"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",
"viash_version" : "0.9.3",
"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",
"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",

24
target/nextflow/sync_resources/.config.vsh.yaml
View File

@@ -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"
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
viash_version: "0.9.4"
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:

81
target/nextflow/sync_resources/main.nf
View File

@@ -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) {
value = value.doubleValue()
} else if (par.type == "float") {
// cast to float if need be
if (value !instanceof Float) {
try {
value = value as Float
} catch (NumberFormatException e) {
expectedClass = "Float"
}
}
if (value instanceof Float) {
value = value.toDouble()
}
expectedClass = value instanceof Double ? null : "Double"
} else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
// cast to boolean if need be
if (value instanceof String) {
def valueLower = value.toLowerCase()
if (valueLower == "true") {
value = true
} else if (valueLower == "false") {
value = false
if (value !instanceof Boolean) {
try {
value = value as Boolean
} catch (Exception e) {
expectedClass = "Boolean"
}
}
expectedClass = value instanceof Boolean ? null : "Boolean"
} else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
// cast to path if need be
if (value instanceof String) {
@@ -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) {
value = value.toString()
if (value !instanceof String) {
try {
value = value as String
} catch (Exception e) {
expectedClass = "String"
}
}
expectedClass = value instanceof String ? null : "String"
} else {
// didn't find a match for par.type
expectedClass = par.type
@@ -3298,16 +3293,17 @@ meta = [
"runner" : "nextflow",
"engine" : "docker|native",
"output" : "target/nextflow/sync_resources",
"viash_version" : "0.9.3",
"git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
"viash_version" : "0.9.4",
"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",
"viash_version" : "0.9.3",
"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",
"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",

24
target/nextflow/untar/.config.vsh.yaml
View File

@@ -181,16 +181,29 @@ build_info:
engine: "docker|native"
output: "target/nextflow/untar"
executable: "target/nextflow/untar/main.nf"
viash_version: "0.9.3"
git_commit: "9ca16ea58d5f010e31714265802c016280594624"
viash_version: "0.9.4"
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:

81
target/nextflow/untar/main.nf
View File

@@ -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) {
value = value.doubleValue()
} else if (par.type == "float") {
// cast to float if need be
if (value !instanceof Float) {
try {
value = value as Float
} catch (NumberFormatException e) {
expectedClass = "Float"
}
}
if (value instanceof Float) {
value = value.toDouble()
}
expectedClass = value instanceof Double ? null : "Double"
} else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
// cast to boolean if need be
if (value instanceof String) {
def valueLower = value.toLowerCase()
if (valueLower == "true") {
value = true
} else if (valueLower == "false") {
value = false
if (value !instanceof Boolean) {
try {
value = value as Boolean
} catch (Exception e) {
expectedClass = "Boolean"
}
}
expectedClass = value instanceof Boolean ? null : "Boolean"
} else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
// cast to path if need be
if (value instanceof String) {
@@ -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) {
value = value.toString()
if (value !instanceof String) {
try {
value = value as String
} catch (Exception e) {
expectedClass = "String"
}
}
expectedClass = value instanceof String ? null : "String"
} else {
// didn't find a match for par.type
expectedClass = par.type
@@ -3277,16 +3272,17 @@ meta = [
"runner" : "nextflow",
"engine" : "docker|native",
"output" : "target/nextflow/untar",
"viash_version" : "0.9.3",
"git_commit" : "9ca16ea58d5f010e31714265802c016280594624",
"viash_version" : "0.9.4",
"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",
"viash_version" : "0.9.3",
"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",
"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",