89 lines
2.3 KiB
Markdown
89 lines
2.3 KiB
Markdown
|
|
||
|
|
|
||
|
|
# 🛝📦 playground
|
||
|
|
|
||
|
|
[](https://github.com/viash-hub/playground)
|
||
|
|
[](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).
|