Lead Omics Workflow Engineer

(ID: 2026-1406)

Axle is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations nationally and abroad. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques to empower decision-making and accelerate research discoveries. We work with some of the top research organizations and facilities in the country including multiple institutes at the National Institutes of Health (NIH).

Benefits We Offer:

• 100% Medical, Dental & Vision Coverage for Employees

• Paid Time Off and Paid Holidays

• 401K match up to 5%

• Educational Benefits for Career Growth

• Employee Referral Bonus

• Flexible Spending Accounts:

• Healthcare (FSA)

• Parking Reimbursement Account (PRK)

• Dependent Care Assistant Program (DCAP)

• Transportation Reimbursement Account (TRN)

The Opportunity: Your Impact

We are seeking a Lead Omics Workflow Engineer to own the technical lifecycle of our client’s omics pipeline estate. You will inherit a library of approximately 20 existing Nextflow pipelines and lead the effort to assess their structure, update their dependencies, and, most importantly, build a comprehensive automated validation framework.

This role requires a unique hybrid of a software architect and a bioinformatics scientist. You will be responsible for ensuring that when tools are upgraded, the scientific results remain stable and reproducible. You will lead a specialized team to deliver a production-ready suite of pipelines that define the standard for excellence in the industry.

About the Mission:

We are partnering with a global leader in drug discovery to modernize the engine of their genomic research. As part of a large-scale digital transformation, we are building and refining the pipelines that process vast amounts of high-throughput omics data.

The goal is simple but ambitious: to ensure that scientific decision-making is supported by a robust, validated, and highly maintainable computational infrastructure. This involves architecting a durable “Omics Workbench” that allows researchers to adapt to new technologies without disrupting core discovery workflows.

What You’ll Do:

• Pipeline Estate Ownership: Perform a structured review of the existing 20+ Nextflow-based omics pipelines, characterizing their dependencies, execution patterns, and known failure modes.

• Architect Comprehensive Test Suites: Lead the design and implementation of a unified test suite that includes representative datasets and regression checks to detect unintended changes in scientific results.

• Lead Tooling & Library Upgrades: Propose and implement updates to pipeline dependencies and container images, ensuring all tools are current while adhering to strict security and support requirements.

• Drive Automated Validation: Oversee the implementation of automated workflows that can execute test suites across the entire pipeline library on-demand or in response to code changes.

• Verify Scientific Consistency: Analyze test reports to confirm that updated pipelines continue to meet agreed-upon scientific and performance criteria, providing expert interpretation of differences found during validation.

• Multi-Infrastructure Execution: Ensure that pipelines remain hermetic and portable across diverse environments, including on-premise SLURM-based HPC clusters and Google Cloud Platform (GCP).

What You’ll Bring (Required Qualifications):

• Lead-Level Technical Authority: Extensive experience managing or leading the development of bioinformatics pipelines in a production or large-scale research setting.

• Nextflow Expert: Mastery of Nextflow for complex workflow orchestration, including advanced configuration, modular design, and execution at scale.

• Omics Domain Depth: Deep understanding of the scientific purpose and library dependencies of common omics pipelines (e.g., RNA-seq, WGS, Proteomics).

• Validation Rigor: A strong background in software testing principles, specifically as they apply to bioinformatics (regression testing, unit testing, and benchmarking).

• Infrastructure & DevOps: Proficiency with Linux/Unix, HPC schedulers (SLURM), and Containerization (Docker/Singularity).

• A “Craftsman” Mindset: A passion for building stateless, modular, and elegant code that separates scientific logic from infrastructure.

What Sets You Apart (Preferred Qualifications):

• Experience in Pharma R&D or high-throughput clinical genomics environments.

• Familiarity with GCP Workflows and cloud-native data orchestration.

• Experience working with large-scale PostgreSQL or other system-of-record scientific databases.

• Contributions to open-source bioinformatics tools or communities (e.g., nf-core)

Disclaimer: The above description is meant to illustrate the general nature of work and level of effort being performed by individuals assigned to this position or job description. This is not restricted as a complete list of all skills, responsibilities, duties, and/or assignments required. Individuals may be required to perform duties outside of their position, job description or responsibilities as needed.

The diversity of Axle’s employees is a tremendous asset. We are firmly committed to providing equal opportunity in all aspects of employment and will not tolerate any illegal discrimination or harassment based on age, race, gender, religion, national origin, disability, marital status, covered veteran status, sexual orientation, status with respect to public assistance, and other characteristics protected under state, federal, or local law and to deter those who aid, abet, or induce discrimination or coerce others to discriminate.

Accessibility: If you need an accommodation as part of the employment process please contact: [email protected]

This role has a market-competitive salary with an anticipated base compensation range listed below. Actual salaries will vary depending on a candidate’s experience, qualifications, skills, and location.

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Salary Range
$125,000—$150,000 USD