🛝📦 playground

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:

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:

./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.

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):

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.
• Discussions: Join our discussions via GitHub Discussions.