Senior Pipeline Engineer

Summary

Join Natera's Platform group as a Senior Pipeline Engineer and become part of a collaborative team developing a scalable platform for next-generation clinical assays. You will play a key role in designing, developing, and architecting software products for the clinical laboratory, contributing to R&D, bioinformatics, and high-performance computing. This position requires expertise in various tech stacks and a passion for building robust and scalable software that directly impacts patient care. The ideal candidate will build CI/CD systems and bioinformatics workflows, creating standardized code repositories and implementing automated pipelines. You will also develop modular components for genomic data processing. Natera offers competitive benefits, including comprehensive medical, dental, vision, life and disability plans, free testing for employees and their families, fertility care benefits, and more.

Requirements

• BS in Computer Science or equivalent program
• 7+ years of experience in software development
• Strong experience with GitHub Actions workflows and pipeline optimization
• Experience with Nextflow and Argo workflows
• Docker expertise, including multi-stage builds
• Knowledge of artifact management systems (Artifactory, AWS ECR)
• Experience with AWS Batch or similar cloud computing solutions
• Proficiency with Git workflows, branch protection, and PR automation
• Ability to develop automated testing frameworks for scientific pipelines
• Understanding of distributed computing principles for large dataset processing

Responsibilities

• Design, develop, and architect software products relevant to the clinical laboratory
• Contribute to cutting-edge R&D, bioinformatics, and high-performance computing initiatives
• Build CI/CD systems and bioinformatics workflows
• Create standardized code repositories
• Implement automated build and test pipelines
• Develop modular Nextflow components for genomic data processing that run reliably at scale

Preferred Qualifications

• Knowledge of common genomics data formats and tools
• Experience with GitHub Actions, GitLab CI
• Experience with Nextflow DSL2 and nf-core modules
• Experience with Docker, Singularity containers
• Experience with AWS ECR, Batch, S3, Lambda
• Experience with Python for pipeline utilities
• Experience with ArgoCD for GitOps deployments
• Experience with AWS CodePipeline

Benefits

• Comprehensive medical, dental, vision, life and disability plans for eligible employees and their dependents
• Free testing in addition to fertility care benefits
• Pregnancy and baby bonding leave
• 401k benefits
• Commuter benefits
• Generous employee referral program