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Portable WDL workflows for IDseq production pipelines

Home Page: https://idseq.net/

License: MIT License

Makefile 0.03% WDL 14.92% Shell 0.24% Python 80.77% Dockerfile 0.98% Awk 0.09% Jupyter Notebook 2.96%

idseq-workflows's Introduction

idseq-workflows - portable IDseq production pipeline logic

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.

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).

idseq-workflows's People

Contributors

yunfangjuan avatar kislyuk avatar morsecodist avatar cdebourcy avatar jshoe avatar mlin avatar gregdingle avatar davidrissato avatar tfrcarvalho avatar markazhang avatar lvreynoso avatar emilyzhong avatar jameshowardwang avatar katrinakalantar avatar meera-srinivasan avatar j-x-han avatar boris-dimitrov avatar mbarrien avatar

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