Our workflow is decidedly uncool and old-fashioned. Scripts produce figures as PDF files. We aim to have the script produce more-or-less final figures, but som

Our workflow is decidedly uncool and old-fashioned. Scripts produce figures as PDF files. We aim to have the script produce more-or-less final figures, but sometimes the last 5-10% is easier to do manually. We don't bother putting them into the manuscript text while editing, and the captions are usually on a separate page, as most of our target journals seem to require. The manuscript gets written in Word + Endnote, with ad-hoc figure reference like See Figure XXX_DOSE_RESPONSE_XXX that get find-replaced at the very end. This is definitely a local optima (if that!), but works pretty well for us especially since it's a pretty diverse group: some computationally-minded folks might be happier with LaTex, but we've also got 85 year old prof, DoD folks, etc who want track changes and familiarity.