README.qmd

---
format: gfm
---
```{r setup, include=FALSE}
project <- yaml::read_yaml("_viash.yaml")
```
# 🛝📦 `r project$name`

[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2F`r project$name`-blue)](`r project$links$repository`) 
[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", project$viash_version)`-blue)](https://viash.io)

`r project$description`

## 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}
#| eval: false
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}
#| eval: false
./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}
#| eval: false
viash ns build --parallel --setup cachedbuild
```

::: {.callout-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}
#| eval: false
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](`r project$links$issue_tracker`).
- **Discussions**: Join our discussions via [GitHub Discussions](`r project$links$repository`/discussions).