idseq-workflows - portable IDseq production pipeline logic

Please see https://github.com/chanzuckerberg/czid-workflows for CZ ID workflows. This repository is no longer maintained.

Infectious Disease Sequencing Platform

IDseq is a hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data.

• Discover - Identify the pathogen landscape
• Detect - Monitor and review potential outbreaks
• Decipher - Find potential infecting organisms in large datasets

IDseq is a collaborative open project of Chan Zuckerberg Initiative and Chan Zuckerberg Biohub.

Running these workflows

This repository contains WDL workflows that the IDseq platform uses in production. See Running WDL workflows locally to get started with them.

CI/CD

We use GitHub Actions for CI/CD. Lint and unit tests run on GitHub from jobs in .github/workflows/wdl-ci.yml (triggered on every commit).