Bioinformatics Engineer - Nextflow And AWS Specialist

We are seeking an experienced Senior Bioinformatics Engineer with deep expertise in Nextflow, AWS cloud infrastructure, and containerized workflow development. This role is ideal for someone who can architect, optimize, and scale production-grade bioinformatics pipelines while collaborating across engineering and scientific teams. You will be responsible for building resilient, high-performance workflow systems that support large-scale NGS data processing.

This position requires availability to work within Pacific Time (PST) hours.

What You’ll Do

• Architect and develop advanced Nextflow pipelines for NGS data processing, analysis, and multi-step workflow orchestration.
• Deploy, operate, and optimize pipelines on AWS EKS and Batch.
• Build and maintain Docker-based container environments for reproducible and portable bioinformatics pipelines.
• Develop and maintain robust Python tooling to support workflow automation, QC reporting, monitoring, and data integration.
• Implement workflow observability, logging, and cost-optimized execution strategies for large-scale genomic data.
• Collaborate with sequencing, bioinformatics, and platform engineering teams to improve workflow reliability and performance.
• Establish best practices for pipeline versioning, continuous integration, automated testing, and cloud-based deployment.
• Ensure pipelines are highly reproducible, fault-tolerant, and suitable for production environments in regulated or high-stakes settings.

What You’ll Bring

Required Qualifications

• 5+ years of experience in bioinformatics, computational biology, workflow engineering, or related fields.
• Expert-level proficiency in Nextflow, including DSL2, modules, workflow optimization, and pipeline debugging.
• Strong hands-on experience with AWS, particularly:
  • EC2 compute environments
  • S3 for cloud storage
  • EKS for workflow execution
• Deep expertise with Docker, including custom image creation, multi-stage builds, and best practices for pipeline reproducibility.
• Strong Python development skills with production-level experience, testing frameworks, packaging, and tooling.
• Experience operating in cloud-native environments with distributed computing, autoscaling, cost-optimization, and workflow orchestration.
• Solid understanding of NGS data formats, sequencing workflows, and common bioinformatics tools.
• Strong Linux skills and experience with CI/CD systems.
• Ability to work effectively in PST time zone (remote or onsite).

Nice to Have

• Experience with Java/Groovy
• Experience building and using APIs
• Experience with Nextflow Tower or similar workflow management platforms.
• Experience configuring Kubernetes workloads for genomics pipelines.
• Background in synthetic biology, DNA design, or high-throughput genomic library analysis.
• Experience collaborating with wet labs or platform teams on sequencing pipeline requirements.