Lead Bioinformatics Pipeline Engineer (Cloud, WDL/Nextflow)

Natera; San Carlos (CA); On-site; USD 144,000 - 180,000; Full time

Benefits offered by this job

Annual bonus

Long‑term equity awards

Health benefits

401(k) with company match

Paid time off and holidays

Wellness and work‑life benefits

Job summary

Natera is seeking a Lead Bioinformatics Engineer to own pipeline and infrastructure engineering for a research informatics team working on cfDNA screening in Women’s and Organ Health. The role is an individual contributor position focused on building robust pipelines and scalable infrastructure on AWS.

You will own WDL workflows, drive the Nextflow transition, and manage the team’s AWS infrastructure as code with Terraform.

Qualifications

• 4+ years of software or pipeline engineering experience in life sciences or related field

Responsibilities

• Maintain and improve WDL workflows on AWS Batch and HealthOmics
• Own Nextflow migration and unify tooling for pipelines
• Improve reliability, observability, and testing across compute environments
• Build internal tooling to reduce manual work and support triage of production issues
• Review agent‑written code to the same standard as your own and decide which tools to adopt
• Collaborate with science leads and data scientists to productionize methods and enable handoff to production
• Use agent-assisted development as part of engineering practices

Skills

Python

Software engineering

Testing and debugging

Workflow systems

AWS Cloud

Infrastructure as code

Observability

Code review

Documentation

AI-assisted workflows

Education

Bioinformatics / Computer Science (degree acceptable option)

Tools

AWS

Terraform

Nextflow

WDL

Snakemake

CWL

Linux

Docker

Kubernetes

Git

Job description

Natera is seeking a Lead Bioinformatics Engineer to own pipeline and infrastructure engineering for a research informatics team working on cfDNA screening in Women’s and Organ Health. The role is an individual contributor position focused on building robust pipelines and scalable infrastructure on AWS.

You will own WDL workflows, drive the Nextflow transition, and manage the team’s AWS infrastructure as code with Terraform.