Automating the State of the Environment Report: A reproducible workflow with Galaxy

As part of the work WG-EMM (WG-EMM-2024/38; SC-CAMLR-43/BG/08 Rev. 1), a standardized report template for the state of the environment in area 48 has been proposed. To facilitate production of the report and ensure reproducibility of the variables’ visualization, we present an automated approach based on the use of the Galaxy platform. This method capitalizes on a recent Galaxy feature: the use of Jupyter notebooks within analytical workflows. It allows for the design of modular scripts in R or Python that can be integrated into complete workflows, which can then be efficiently automated. Based on open-source technologies and in line with the FAIR (Findable, Accessible, Interoperable, Reusable) principles, this approach standardizes analyses and ensures data confidentiality. It represents a first step towards the development of a common, reproducible and modular toolbox for ecosystem monitoring in Antarctica.