{"repo":"stjudecloud/workflows","free":true,"listed":false,"github":"https://github.com/stjudecloud/workflows","clone":"git clone https://github.com/stjudecloud/workflows.git","description":"Bioinformatics workflows developed for and used on the St. Jude Cloud project.","language":"WDL","stars":44,"topics":["bioinformatics-workflows","workflows","cromwell","wdl","bioinformatics","computational-biology","workflow","workflow-engine","next-generation-sequencing","genomics"],"license":"MIT","category":"workflow-automation","readme_excerpt":"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. Resources requirements have been optimized to minimize failures in our computing environment, but they may not reflect the best settings for your use case. Please ensure that you tailor these parameters to fit your needs. 🏠 Homepage Our documentation is generated with Sprocket. Repository Structure The repository is laid out as follows: workflows/ - Directory containing all end-to-end bioinformatics workflows. tools/ - All tools we have wrapped as individual WDL tasks. data structures/ - WDL struct definitions and tasks or workflows related to their construction, parsing, or validation. docker/ - Dockerfiles used in our workflows. All docker images are published to the GitHub Container Registry as a part of our CI and are versioned. scripts/ - This directory is passed to the docker build step as a context, and contains scripts that can be copied to our docker containers. test/fixtures/ - Home to all of our test fixtures. We use Sprocket's test command for validating our code. Note that this directory is quite large by Git standards, and we intend to prune it or otherwise reduce its size in the future. developer scripts - Home to any scripts that ease the development process. Expected FASTQ file name conventions The tasks and workflows in this repository which have one o","default_branch":null,"files":null,"tree":[],"storefront":"/r/stjudecloud","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/stjudecloud/workflows/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}