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https://github.com/chanzuckerberg/idseq-workflows
Portable WDL workflows for IDseq production pipelines
https://github.com/chanzuckerberg/idseq-workflows
Last synced: 3 days ago
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Portable WDL workflows for IDseq production pipelines
- Host: GitHub
- URL: https://github.com/chanzuckerberg/idseq-workflows
- Owner: chanzuckerberg
- License: mit
- Archived: true
- Created: 2019-10-17T05:00:27.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2022-01-19T22:34:53.000Z (almost 3 years ago)
- Last Synced: 2023-10-25T20:37:22.088Z (about 1 year ago)
- Language: Python
- Homepage: https://idseq.net/
- Size: 46.5 MB
- Stars: 30
- Watchers: 14
- Forks: 12
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
- awesome_ai_agents - Idseq-Workflows - Portable WDL workflows for IDseq production pipelines (Building / Workflows)
- awesome_ai_agents - Idseq-Workflows - Portable WDL workflows for IDseq production pipelines (Building / Workflows)
README
# 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 This repository is no longer maintained.----------------------------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 datasetsIDseq 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).