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https://github.com/chanzuckerberg/idseq-workflows

Portable WDL workflows for IDseq production pipelines
https://github.com/chanzuckerberg/idseq-workflows

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Portable WDL workflows for IDseq production pipelines

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# idseq-workflows - portable IDseq production pipeline logic

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 This repository is no longer maintained.

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#### 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](https://www.chanzuckerberg.com/) and
[Chan Zuckerberg Biohub](https://czbiohub.org).

## Running these workflows
This repository contains [WDL](https://openwdl.org/) workflows that the [IDseq](https://idseq.net/) platform uses in
production. See [Running WDL workflows locally](https://github.com/chanzuckerberg/idseq-workflows/wiki/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).