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harrispopgen / mutyper

Ancestral k-mer mutation types for SNP data
https://harrispopgen.github.io/mutyper/
MIT License
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Fix references in https://github.com/harrispopgen/mutyper/blob/master/paper/paper.md #42

Closed izabelcavassim closed 1 year ago

izabelcavassim commented 1 year ago

In the session Applications of their article, the authors give examples of where users have utilized mutyper but the authors have not shared the specific citations for these articles. I would like to see references for the work they have mentioned, specifically: @sasani2022 and @Vollger2022.

wsdewitt commented 1 year ago

My understanding was that the markdown source file should have an empty References section, but then the JOSS editorialbot compiles the paper pdf using the bibtext file to fill in the references cited (with tags like @sasani2022). It looks like the references are rendering in the pdf compiled from the markdown + bibtext file, linked by the editorialbot comment here: https://github.com/openjournals/joss-reviews/issues/5227#issuecomment-1458443035.

Does this look ok?

izabelcavassim commented 1 year ago

sorry that works, are you intending to leave the markdown in the repo too? Is there a way to print it out to markdown or only when rendered to pdf? I guess if you create references manually on markdown it would be overwritten by the pdf? I never tried so I don't know.

wsdewitt commented 1 year ago

We haven't found a way to also render the references in the formatted markdown, but in PR #47 we've added a README in the paper/ subdirectory to explain that the markdown paper and bibtex references are source files for a pdf paper build. We also provide a link to the JOSS review page (where the pdf paper would appear).