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 -y
conda activate workflows-dev
git clone [email protected]:stjudecloud/workflows.git
cd workflowsAny 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.jsonRepository Structure
The repository is laid out as follows:
bin- Scripts used by Cromwell configuration settings. Add this to$PATHprior to using configurations inconfwith 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 as a part of our CI and are versioned.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 |
|---|---|---|---|---|---|
| RNA-Seq Standard | v2.0.0 | Standard RNA-Seq harmonization pipeline. | Specification | Realign BAM Workflow, FastQ Workflow |  |
| Build STAR References | N/A | Build STAR aligner reference files used in RNA-Seq Standard harmonization pipelines. | None | Workflow | |
| Quality Check Standard | v1.0.0 | Perform ~10 different QC analyses on a BAM file and compile the results using MultiQC. | Specification | Workflow | |
| Build FastQ Screen References | N/A | Build references used in WGS/WES Quality Check pipeline for running FastQ Screen. | None | Workflow | |
| ESTIMATE | v1.0.0 (beta) | Runs the ESTIMATE software package on a feature counts file. | None | Workflow |  |
| Calculate Gene Lengths | N/A | Produces a gene length file from a GTF. | None | Workflow | |
| Build BWA References | N/A | Builds reference files used by the BWA aligner. | None | Workflow | |
| BAM to FastQs | v1.0.0 | Split a BAM file into read groups, then read 1 FastQs and read 2 FastQs. | None | Workflow | |
Author
- 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.
📝 License
Copyright © 2020-Present St. Jude Cloud Team.
This project is MIT licensed.