Dr Magdalena Antczak

Beyond the pipeline: building bioinformatics workflows for non-bioinformaticians

Dr. Magdalena Antczak1, Dr. Cameron J Hyde2, Lanxi (Daisy) Li2, Valentine Murigneux1, Dr. Sarah Williams1, W C Mike Thang1, Bradley Pease3, Shaun Bochow3, Grace Sun3 

  1. QCIF Bioinformatics, Brisbane, Queensland, Australia 
  2. QCIF Data and Software Solutions, Brisbane, Queensland, Australia
  3. Department of Agriculture, Fisheries and Forestry, Australian Government

Creating bioinformatics workflows that can be adopted by an organisation full of non-bioinformaticians requires more than robust code – it demands a deliberate blend of technical precision, user-driven design, iterative refinement, and deep stakeholder engagement. In collaboration with the Australian Department of Agriculture, Fisheries and Forestry (DAFF), we set out to build a per-sample taxonomic identification workflow presented in a clear, accessible, and informative way.

Central to this is a dynamic user-friendly HTML report featuring interactive components such as sortable tables, clickable rows, and an interactive phylogenetic tree viewer. Accessibility and automation were identified as a priority early in the project. We used Nextflow for workflow orchestration and adopted modular design and containerisation. Rather than building a monolithic system, we focused on demonstrating a functional minimal viable product (MVP) early, enabling DAFF analysts to test, critique, and actively shape features throughout development.

While this approach yielded a reproducible and scalable pipeline, the process also revealed several lessons for future efforts. Chief among these were the need for regular user engagement and shorter iteration cycle to integrate feedback swiftly and guide development. Equally critical was the need for concise reporting with digestible summaries of complex outcomes.

This talk will highlight how reproducibility and accessibility rely on thoughtful process design – especially when delivering complex bioinformatics tools to general users. It will share the lessons learned, design principles and stakeholder engagement that helped bridge the gap between bioinformatics and usability.

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