Lead Omics Workflow Engineer

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)