Introduction
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:ref:`Standard Operating Procedures (SOPs) <standard_operating_procedure_sop>` are detailed, written instructions that describe how to perform specific tasks or processes consistently and correctly. SOPs are essential for ensuring quality, accuracy, and reproducibility in various settings, particularly in regulated environments such as clinical laboratories.

The use of SOPs in clinical laboratories has traditionally focused on wet-laboratory procedures, where they provide step-by-step guidance for laboratory personnel to follow when performing diagnostic procedures. Examples of such procedures (within a public health context) could include, the culture and identification of *Mycobacterium tuberculosis* (TB) or the detection of HIV using serological assays. As such the evolution of SOPs has historically been closely tied to physical laboratory workflows. However, as genomics becomes an ever more integral part of disease diagnostics and pathogen surveillance, there is an increasing need for SOPs tailored specifically to bioinformatics pipelines. 

Unlike laboratory SOPs, which focus on physical procedures and equipment, bioinformatics SOPs must describe digital workflows, computational tools, data management processes, and software dependencies. Consequently existing SOP structures and formats designed for wet-lab procedures may not be fully appropriate for documenting bioinformatics workflows. Existing SOP templates are also unsuited to the diverse range of other procedures that may require SOP documentation within a modern clinical laboratory setting. For example, SOPs may be needed to document staff training procedures, code update and review processes for software, or verification and validation protocols for new analytical methods or examinations.