Build branch main with version main (861319f)

Build pipeline: vsh-ci-template-8vdc6

Source commit: 861319f5dd

Source message: Merge pull request #4 from viash-hub/update-star-align-params

update param

README.md

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+
+
+# 🛝📦 playground
+
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fplayground-blue.png)](https://github.com/viash-hub/playground)
+[![Viash
+version](https://img.shields.io/badge/Viash-v0.9.0--RC6-blue)](https://viash.io)
+
+A collection of bioinformatics pipelines to illustrate the use of biobox
+(and biotools).
+
+## Quickstart
+
+### Requirements
+
+To run the components and workflows included in this repository, you
+need to have the following software installed:
+
+- Bash (\>= 3.2) or an equivalent shell
+- Java Development Kit (\>= 12)
+- Docker
+- Viash (\>= 0.6.7)
+- Nextflow (\>= 21.04)
+
+### Cloning the repository
+
+To clone this repository to your local machine, copy the URL of the
+forked repository by clicking the green “Code” button and selecting
+HTTPS or SSH. In your terminal or command prompt, navigate to the
+directory where you want to clone the repository and enter the following
+command:
+
+``` bash
+git clone <copied_url> playground
+cd playground
+```
+
+### Test dataset
+
+You will also need to download the test resources by running the
+following command. From the repository root, run:
+
+``` bash
+./test_data.sh
+```
+
+This will create the `test_data` folder and a file called
+`params_file.yaml`; the latter can be used to run the worklow with the
+generated test data.
+
+### Building
+
+Before running the workflow, the viash components need to be build and
+the docker images generated.
+
+``` bash
+viash ns build --parallel --setup cachedbuild
+```
+
+> [!NOTE]
+>
+> The `--setup cachedbuild` enables building the docker images.
+
+You will now see a `target` folder inside the root of the repository.
+
+### Testing the workflow
+
+To use the workflow with test data, use the following command (from the
+root of the repository):
+
+``` bash
+nextflow run . -main-script ./target/nextflow/mapping_and_qc/main.nf \
+-params-file ./params_file.yaml \
+-profile docker \
+-c ./target/nextflow/mapping_and_qc/nextflow.config
+```
+
+The output will be written to the folder `test_run_output`, as specified
+in the `publish_dir` argument in the `params_file.yaml`.
+
+## 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/playground/issues).
+- **Discussions**: Join our discussions via [GitHub
+  Discussions](https://github.com/viash-hub/playground/discussions).