Axle · 2 weeks ago
Lead Omics Workflow Engineer
United States
Full-time
Remote
Senior Level, Lead/Staff
$125K/yr - $150K/yrAxle is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications. They are seeking a Lead Omics Workflow Engineer to own the technical lifecycle of client’s omics pipeline estate, ensuring scientific results remain stable and reproducible while leading a specialized team to deliver a production-ready suite of pipelines.
BiotechnologyHealth CareInformation TechnologySoftware
Responsibilities
Perform a structured review of the existing 20+ Nextflow-based omics pipelines, characterizing their dependencies, execution patterns, and known failure modes
Lead the design and implementation of a unified test suite that includes representative datasets and regression checks to detect unintended changes in scientific results
Propose and implement updates to pipeline dependencies and container images, ensuring all tools are current while adhering to strict security and support requirements
Oversee the implementation of automated workflows that can execute test suites across the entire pipeline library on-demand or in response to code changes
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
Ensure that pipelines remain hermetic and portable across diverse environments, including on-premise SLURM-based HPC clusters and Google Cloud Platform (GCP)
Qualification
Required
Extensive experience managing or leading the development of bioinformatics pipelines in a production or large-scale research setting
Mastery of Nextflow for complex workflow orchestration, including advanced configuration, modular design, and execution at scale
Deep understanding of the scientific purpose and library dependencies of common omics pipelines (e.g., RNA-seq, WGS, Proteomics)
A strong background in software testing principles, specifically as they apply to bioinformatics (regression testing, unit testing, and benchmarking)
Proficiency with Linux/Unix, HPC schedulers (SLURM), and Containerization (Docker/Singularity)
A passion for building stateless, modular, and elegant code that separates scientific logic from infrastructure
Preferred
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)
Benefits
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)
Company
Axle
At Axle, we are driven by the mission to accelerate discovery and enhance organizational outcomes by revolutionizing operations with our innovative solutions.
Founded in 2002
501-1000 employees
H1B Sponsorship
Axle has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
Represents job field similar to this job
Trends of Total Sponsorships
2025 (37)
2024 (40)
2023 (61)
2022 (30)
2021 (19)
2020 (38)
Funding
Current Stage
Late StageLeadership Team
Gary Mays
Chief Operating Officer
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