This report discusses 3 distinct, but overlapping topics. Firstly, it recommends the tools and best practices for research software engineering and data science that are most relevant to the researchers working on the Wales Multimorbidity Machine Learning (WMML) project. Secondly, it expands upon these recommendations for the specific use case of Trusted Research Environments (TREs), with development workflows for computational research in TREs offered that respect and complement existing best practices. Finally, it discusses the considerations around publishing research code that is developed to run within a TRE on sensitive data, offering practical advice that researchers using TREs can follow.