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f00709ee19
Build pipeline: vsh-ci-build-template-xfb9n
Source commit: b74f55253e
Source message: Prepare for 0.3.2 release (#19)
143 lines
4.4 KiB
Markdown
143 lines
4.4 KiB
Markdown
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# 🪡📦 craftbox
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[](https://www.viash-hub.com/packages/craftbox)
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[](https://github.com/viash-hub/craftbox)
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[](https://github.com/viash-hub/craftbox/blob/main/LICENSE)
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[](https://github.com/viash-hub/craftbox/issues)
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[](https://viash.io)
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A collection of custom-tailored scripts and applied utilities built with
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Viash.
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## Introduction
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`craftbox` is a curated collection of custom scripts and utilities
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designed to tackle context-specific tasks.
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Emphasizing the Viash principles, `craftbox` components aim for
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**reusability**, **reproducibility**, and adherence to **best
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practices**. Key features generally include:
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- **Standalone & Nextflow Ready:** Components are built to run directly
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via the command line or be smoothly integrated into Nextflow
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workflows.
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- **Custom Implementations:** Contains scripts and tools developed for
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particular tasks that may not be found in broader collections.
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- **High Quality Standards (promoted by Viash):**
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- Clear documentation for components and their parameters.
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- Full exposure of underlying script/tool arguments for fine-grained
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control.
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- Containerized (Docker) to ensure dependency management and a
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consistent, reproducible runtime environment.
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- Unit tested where applicable to ensure components function as
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expected.
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## Example Usage
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Viash components in craftbox can be run in various ways:
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``` mermaid lang="mermaid
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flowchart TD
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A[craftbox v0.3.2] --> B(Viash Hub Launch)
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A --> C(Viash CLI)
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A --> D(Nextflow CLI)
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A --> E(Seqera Cloud)
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A --> F(As a dependency)
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```
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### 1. Via the Viash Hub Launch interface
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You can run this component directly from the Viash Hub [Launch
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interface](https://www.viash-hub.com/launch?package=craftbox&version=v0.3.2&component=concat_rtext&runner=Executable).
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### 2. Via the Viash CLI
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You can run this component directly from the command line using the
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Viash CLI.
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``` bash
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viash run vsh://craftbox@v0.3.2/concat_rtext -- --help
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viash run vsh://craftbox@v0.3.2/concat_rtext -- \
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--input path/to/input.txt \
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--input path/to/compressed.txt.gz \
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--output path/to/output.txt
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```
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This will run the component with the specified input files and output
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the results to the specified output file.
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### 3. Via the Nextflow CLI or Seqera Cloud
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You can run this component as a Nextflow pipeline.
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``` bash
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nextflow run https://packages.viash-hub.com/vsh/craftbox \
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-revision v0.3.2 \
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-main-script target/nextflow/concat_rtext/main.nf \
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-latest -resume \
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-profile docker \
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--input "path/to/input.txt;path/to/compressed.txt.gz" \
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--output path/to/output.txt
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```
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**Note:** Make sure that the [Nextflow
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SCM](https://www.nextflow.io/docs/latest/git.html#git-configuration) is
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set up properly. You can do this by adding the following lines to your
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`~/.nextflow/scm` file:
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``` groovy
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providers.vsh.platform = 'gitlab'
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providers.vsh.server = 'https://packages.viash-hub.com'
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```
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**Tip:** This will also work with Seqera Cloud or other
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Nextflow-compatible platforms.
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### 4. As a dependency
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In your Viash config file (`config.vsh.yaml`), you can add this
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component as a dependency:
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``` yaml
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dependencies:
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- name: concat_rtext
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repository: vsh://craftbox@v0.3.2
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```
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**Tip:** See the [Viash
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documentation](https://viash.io/guide/nextflow_vdsl3/create-a-pipeline.html#pipeline-as-a-component)
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for more details on how to use Viash components as a dependency in your
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own Nextflow workflows.
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## Contributing
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Contributions are welcome! We aim to build a comprehensive collection of
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high-quality bioinformatics components. If you’d like to contribute,
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please follow these general steps:
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1. Find a component to contribute
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2. Add config template
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3. Fill in the metadata
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4. Find a suitable container
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5. Create help file
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6. Create or fetch test data
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7. Add arguments for the input files
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8. Add arguments for the output files
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9. Add arguments for the other arguments
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10. Add a Docker engine
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11. Write a runner script
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12. Create test script
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13. Create a `/var/software_versions.txt` file
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See the
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[CONTRIBUTING](https://github.com/viash-hub/craftbox/blob/main/CONTRIBUTING.md)
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file for more details.
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