CI
36b9c79457
Build pipeline: viash-hub.toolbox.main-4f6nw
Source commit: d33eb37068
Source message: Update readme and package config (#13)
* update readme and package config
* update changelog
* update readme
* update readme
* fix url
* make images relative again
140 lines
4.3 KiB
Markdown
140 lines
4.3 KiB
Markdown
|
||
|
||
# 🛠📦 toolbox
|
||
|
||
[](https://www.viash-hub.com/packages/toolbox)
|
||
[](https://github.com/viash-hub/toolbox)
|
||
[](https://github.com/viash-hub/toolbox/blob/main/LICENSE)
|
||
[](https://github.com/viash-hub/toolbox/issues)
|
||
[](https://viash.io)
|
||
|
||
A collection of curated command-line tools for general IT tasks, built
|
||
with Viash.
|
||
|
||
## Introduction
|
||
|
||
`toolbox` provides a versatile suite of IT components, following the
|
||
robust Viash (https://viash.io) framework. This package focuses on
|
||
delivering reliable, standalone tools that can be easily integrated into
|
||
larger computational workflows.
|
||
|
||
The core philosophy emphasizes **reusability**, **reproducibility**, and
|
||
adherence to **best practices** in component creation. Key features of
|
||
`toolbox` components include:
|
||
|
||
- **Standalone & Nextflow Ready:** Execute components directly from the
|
||
command line or seamlessly incorporate them into Nextflow workflows.
|
||
- **High Quality Standards:**
|
||
- Comprehensive documentation for each component and its parameters.
|
||
- Full exposure of the underlying tool’s arguments for maximum
|
||
flexibility.
|
||
- Containerized (Docker) to ensure consistent environments and manage
|
||
dependencies, leading to enhanced reproducibility.
|
||
- Unit tested to verify functionality and ensure reliability.
|
||
|
||
## Example Usage
|
||
|
||
Viash components in toolbox can be run in various ways:
|
||
|
||
``` mermaid lang="mermaid"
|
||
flowchart TD
|
||
A[toolbox v0.1.0] --> 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=toolbox&version=v0.1.0&component=yq&runner=Executable).
|
||
|
||
|
||
|
||
### 2. Via the Viash CLI
|
||
|
||
You can run this component directly from the command line using the
|
||
Viash CLI.
|
||
|
||
``` bash
|
||
viash run vsh://toolbox@v0.1.0/yq -- --help
|
||
|
||
viash run vsh://toolbox@v0.1.0/yq -- \
|
||
--input path/to/input.yaml \
|
||
--output output.yaml
|
||
```
|
||
|
||
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/toolbox \
|
||
-revision v0.1.0 \
|
||
-main-script target/nextflow/yq/main.nf \
|
||
-latest -resume \
|
||
-profile docker \
|
||
--input path/to/input.yaml \
|
||
--publish_dir path/to/output
|
||
```
|
||
|
||
**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: yq
|
||
repository: vsh://toolbox@v0.1.0
|
||
```
|
||
|
||
**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
|
||
|
||
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
|
||
3. Fill in the metadata
|
||
4. Find a suitable container
|
||
5. Create help file
|
||
6. Create or fetch test data
|
||
7. Add arguments for the input files
|
||
8. Add arguments for the output files
|
||
9. Add arguments for the other arguments
|
||
10. Add a Docker engine
|
||
11. Write a runner script
|
||
12. Create test script
|
||
13. Create a `/var/software_versions.txt` file
|
||
|
||
See the
|
||
[CONTRIBUTING](https://github.com/viash-hub/toolbox/blob/main/CONTRIBUTING.md)
|
||
file for more details.
|