This repository contains all bioinformatics workflows used on the St. Jude Cloud project. Officially, the repository is in beta — the project is adding workflows as they are developed and put into production.

🏠 Homepage

Getting Started

At the time of writing, all workflows are written in WDL and are tested using Cromwell. We use Oliver to easily interact with the Cromwell server to perform various tasks. Although we do not test outside of Cromwell, we expect that the workflows will work just as well using other runners.

The easiest way to get started is to install bioconda and the run the following commands:

conda create -n workflows-dev -c conda-forge cromwell==47 -y
conda activate workflows-dev
git clone git@github.com:stjudecloud/workflows.git
cd workflows

Any of the workflows in the workflows folder is a good place to start, e.g.

cromwell run workflows/reference/bootstrap-reference.wdl --inputs workflows/reference/inputs.json

Repository Structure

The repository is laid out as follows:

• bin - Scripts used by Cromwell configuration settings. Add this to $PATH prior to using configurations in conf with Cromwell.
• conf - Cromwell configuration files created for various environments that we use across our team. Feel free to use/fork/suggest improvements.
• docker - Dockerfiles used in our workflows. All docker images are published to Docker Hub.
  • At the time of writing, there is only one Docker image heavily in use, which is our bioinformatics base image.
• tools - All tools we have wrapped as individual WDL tasks.
• workflows - Directory containing all end-to-end bioinformatics workflows.

Workflows Available

The current workflows exist in this repo with the following statuses:

Name	Version	Description	Specification	Workflow	Status
Build References	v2.0.0 (beta)	Build reference files used in harmonization pipelines.	None	Workflow
Standard RNA-Seq	v2.0.0 (beta)	Standard RNA-Seq harmonization pipeline.	Specification	Workflow

Author

👤 St. Jude Cloud Team

• Website: https://stjude.cloud
• Github: @stjudecloud
• Twitter: @StJudeResearch

Tests

Given that this repo is still new, there are no tests. When we add tests, we will update the README.

🤝 Contributing

Contributions, issues and feature requests are welcome!
Feel free to check issues page. You can also take a look at the contributing guide.

Versioning

When versioned, workflows will be versioned according to the SemVer guidelines. For now, we do not guarantee that all workflows will have an associated version.

📝 License

Copyright © 2019 St. Jude Cloud Team.
This project is MIT licensed.