5b1018434e
Build pipeline: vsh-ci-template-8vdc6
Source commit: 861319f5dd
Source message: Merge pull request #4 from viash-hub/update-star-align-params
update param
89 lines
2.3 KiB
Markdown
89 lines
2.3 KiB
Markdown
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# 🛝📦 playground
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[](https://github.com/viash-hub/playground)
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[](https://viash.io)
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A collection of bioinformatics pipelines to illustrate the use of biobox
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(and biotools).
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## Quickstart
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### Requirements
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To run the components and workflows included in this repository, you
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need to have the following software installed:
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- Bash (\>= 3.2) or an equivalent shell
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- Java Development Kit (\>= 12)
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- Docker
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- Viash (\>= 0.6.7)
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- Nextflow (\>= 21.04)
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### Cloning the repository
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To clone this repository to your local machine, copy the URL of the
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forked repository by clicking the green “Code” button and selecting
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HTTPS or SSH. In your terminal or command prompt, navigate to the
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directory where you want to clone the repository and enter the following
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command:
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``` bash
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git clone <copied_url> playground
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cd playground
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```
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### Test dataset
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You will also need to download the test resources by running the
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following command. From the repository root, run:
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``` bash
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./test_data.sh
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```
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This will create the `test_data` folder and a file called
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`params_file.yaml`; the latter can be used to run the worklow with the
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generated test data.
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### Building
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Before running the workflow, the viash components need to be build and
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the docker images generated.
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``` bash
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viash ns build --parallel --setup cachedbuild
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```
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> [!NOTE]
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>
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> The `--setup cachedbuild` enables building the docker images.
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You will now see a `target` folder inside the root of the repository.
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### Testing the workflow
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To use the workflow with test data, use the following command (from the
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root of the repository):
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``` bash
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nextflow run . -main-script ./target/nextflow/mapping_and_qc/main.nf \
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-params-file ./params_file.yaml \
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-profile docker \
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-c ./target/nextflow/mapping_and_qc/nextflow.config
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```
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The output will be written to the folder `test_run_output`, as specified
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in the `publish_dir` argument in the `params_file.yaml`.
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## Support and Community
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For support, questions, or to join our community:
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- **Issues**: Submit questions or issues via the [GitHub issue
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tracker](https://github.com/viash-hub/playground/issues).
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- **Discussions**: Join our discussions via [GitHub
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Discussions](https://github.com/viash-hub/playground/discussions).
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