Analyst Programmer (Workflow Automation)

Technology and Innovation

Hong Kong Science Park, Shatin

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With HKGI’s continued expansion, we are seeking an Analyst Programmer (Workflow Automation) to design, operate, and optimise workflow automation for bioinformatics analysis pipelines running on High-Performance Computing (HPC) infrastructure. This role will assist our scientists and curators in accelerating genomic discoveries by ensuring reliable and scalable data processing and sharing. The incumbent will assume the following responsibilities:

Key Responsibilities:

  • Design, develop and maintain an orchestrated platform to support bioinformatics analysis pipelines (e.g. Next-Generation Sequencing, RNA sequencing, variant calling)
  • Develop and refine workflow orchestration logic for scheduling, prioritising, and managing computational jobs across HKGI’s HPC cluster (including job submission, dependency management, retries, scheduling policies and resource optimisation)
  • Collaborate with the Data Warehouse team to build consistent, traceable and interoperable data pathways for sharing and exchange
  • Champion automation and reliability of systems, developing tools for end-to-end pipeline management (monitoring, logging and alerting) to ensure traceability and reproducibility
  • Investigate production pipeline issues, resolve performance bottlenecks, and implement resilient solutions
  • Collaborate with the Infrastructure team to maintain and enhance pipeline-related infrastructure (e.g. execution environments, storage integration, and cluster connectivity)
  • Promote modern software development best practices (Git, CI/CD and code review) for managing pipeline configurations, code versioning, and documentation
  • Uphold data security and privacy requirements to safeguard sensitive genomic data
  • Perform any other duties assigned by senior officer

Requirements:

We are seeking a high-calibre candidate for the post of Analyst Programmer (Workflow Automation) who possesses:

  • A bachelor’s degree or above in Computer Science, Informatics, Bioinformatics, Computational Biology or related fields
  • At least 5 years of experience in software engineering or scientific computing, preferably in large-scale data or high-throughput computation
  • Strong proficiency in at least one programming language (e.g. Python, Java, Go, or C++) and experience in a Linux environment
  • Proven experience with workflow orchestration engines (e.g. Nextflow, Snakemake, WDL/Cromwell, CWL, Airflow, Argo) and understanding of their deployment on HPC or cloud-based systems
  • Hands-on experience with HPC environment and job schedulers, preferably SLURM
  • Solid foundation in version control (Git), automated testing, and CI/CD pipelines
  • Strong sense of ownership, excellent problem-solving skills, and a collaborative mindset

Preferred Skills:

  • Expertise in bioinformatics pipelines and familiarity with common genomic data formats (FASTQ, BAM/CRAM, VCF)
  • Experience with containerisation technologies (Docker, Singularity)
  • Basic knowledge in building monitoring and observability dashboards for pipeline services
  • Experience working with clinical, biomedical or research datasets
  • Solid experience in using AI-assisted coding tools (e.g., GitHub Copilot) to accelerate pipeline development and documentation

Office Location: Hong Kong Science Park, Shatin

Remuneration:
Successful candidate will be offered attractive remuneration and be appointed on an initial two-year contract (subject to mutual agreement for contract renewal).

Application:
Interested parties should send full resume enclosing current and expected remuneration together with availability to recruitment3@genomics.org.hk on or before 30 April 2026. Only shortlisted candidates will be notified.

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