Update citation/publish pipeline

[thorellk]

With the 3.0 release we should update the Zenodo citation so that the correct people are acknowledged. Should we also try to publish the pipeline as some kind of short communication? Or is that to aim too high?

[abhi18av]

I think that this makes sense. While working on my masters, I realized that referencing book/articles is much easier than referencing source code and repositories. When I came across this pipeline I loved this idea and release my own work via zenodo https://zenodo.org/record/4294795

I do think that academically speaking an updated citation for the latest stable version makes things more authentic.

[abhi18av]

And I'm also in favor of following this up with a short communication as well.

[boulund]

I can't remember exactly since it was a while since I set it up, but I think that if we make a release here on github it will be very easy to assign a new DOI using that release.

[abhi18av]

That makes sense, it's almost like a CI/CD. Btw, I'm curious does it parse the commits for list of people who have contributed?

[boulund]

Yes, I think it does

[boulund]

When you've tested that everything works for the 3.0 release in the main branch and all the docs have hade their final touches, can you make a release on github so I can link it into Zenodo?

[emilio-r]

Was there ever any resolution to this? It seems that the docs have been updated already. I am asking as I will be starting to write my thesis very soon and having a DOI then, by which to cite the work with BACTpipe 3.0, would be great.

[boulund]

Someone just needs to make a new release on Github so we can attach a new Zenodo DOI to that release.

[boulund]

Once we merge the pending changes from the develop branch into the main branch I'll make a new release and update the Zenodo stuff

[thorellk]

Hooray 😄

Now when we're happily done with 3.1 maybe it is time to update the citation?

[boulund]

https://zenodo.org/record/4742358#.YJUyvbX7Q-U

[boulund]

I think we missed the citation in the docs,
https://bactpipe.readthedocs.io/en/latest/#citing-bactpipe

can someone make a commit fixing that?