CURATOR: John Goodhue
COMMENT-JG I suggest putting this in the discussion zone for now. This is an important topic area, but needs narrower questions that focus on specific tools or techniques. The remarks from@pdurbin below point to some useful specifics.
Editor remarks - Pdurbin: The question “How do I get my software outputs cited as scholarly work?” sounds a bit like “How do I increase my h-index?” It’s one thing to make your software citable, but it’s quite another to actually get cited. The abstract of “Software citation principles” at https://peerj.com/articles/cs-86/ begins with “Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation.” So it’s an uphill battle. That paper recommends making sure you software has a “unique, persistent, and machine-actionable identifiers such as a DOI, ARK, or PURL” and if your software is on GitHub, the most straightforward way to give it a DOI is to use Zenodo as explained at https://guides.github.com/activities/citable-code/