I used a lot of different tools and strategies to make this paper easily reproducible at different levels. There's Docker container for the highest level of reproducibility, and package versions are managed with renv. The data used in the paper is hosted on Zenodo to avoid long queue times when downloading from the Climate Data Store and future-proof for when it goes away and checksumed before using it.
Metadata annotation is key to reproducibility in sequencing experiments. Reproducing this research using the scripts provided will also show the current level of annotation in years since 2015 when the paper was published.
I tried hard to make this paper as reproducible as possible, but as techniques and dependencies become more complex, it is hard to make it 100% clear. Any form of feedback is more than welcome.