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KThorellGroup / BACTpipe

BACTpipe: An assembly and annotation pipeline for bacterial genomics
https://bactpipe.readthedocs.org
MIT License
20 stars 8 forks source link

Update citation/publish pipeline #137

Open thorellk opened 3 years ago

thorellk commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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

boulund commented 3 years ago

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 commented 3 years ago

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?

image

boulund commented 3 years ago

Yes, I think it does

boulund commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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

boulund commented 3 years ago

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 commented 3 years ago

Hooray 😄

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

boulund commented 3 years ago

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

boulund commented 3 years ago

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

can someone make a commit fixing that?

thorellk commented 3 years ago

Hmm, seems like Sandra is left out and the naming scheme is quite weird, mixing GitHub user id's and full names, including capitalized ones. I guess this is collected from the GitHub user information? Is there any way of editing this?

boulund commented 3 years ago

Yes, it automatically collects the names/usernames of everyone who has contributed commits. It seems we can edit it manually if we want to. We just need to decide which authors should be there and in which order.

thorellk commented 3 years ago

Emilio Rudbeck; Abhinav Sharma; Yue Hu; Joseph Kirangwa; Emilyn Costa Conceição; Sandra Álvarez-Carretero; Fredrik Boulund; Kaisa Thorell? Or if you want to be the last?

boulund commented 3 years ago

That looks fine with me, I'll update the citation on Zenodo and in the docs right away.

boulund commented 3 years ago

I have updated the Zenodo citation and the citation on the first page of the docs, and synced the little commit from master to develop, so we can continue with feature branches from develop for future developments.

thorellk commented 3 years ago

@emilio-r and @abhi18av, were you interested in writing something on the pipeline as well to publish it as some kind of paper?

thorellk commented 3 years ago

@boulund you forgot Sandra! She was the original author of BACTpipe and even if much has changed since I still think she should be included.

boulund commented 3 years ago

I don't understand what you mean, Sandra is included? image

abhi18av commented 3 years ago

I think, that this might be because of the confusion with older Zenodo DOI.

Should we mention the project DOI instead of the release DOI?

1254247

Screenshot 2021-05-09 at 9 29 23 AM
abhi18av commented 3 years ago

@emilio-r and @abhi18av, were you interested in writing something on the pipeline as well to publish it as some kind of paper?

Yup, that'd be great. Perhaps a short publication explaining the workflow and the chioces behind this?

boulund commented 3 years ago

It should be the project DOI (that always points to the latest release on Zenodo) that is embedded in the README

image points to https://zenodo.org/badge/latestdoi/83326100

thorellk commented 3 years ago

Sandra was missing in the docs, not in the Zenodo doi. Sorry for not being clear, I added it now :)

emilio-r commented 3 years ago

First: Huzzah to having released 3.1! :tada:

@emilio-r and @abhi18av, were you interested in writing something on the pipeline as well to publish it as some kind of paper?

Yes, writing something would be a good way to cap this whole experience. Next week I may find some time as my thesis will be in for review. Then I could probably write together a shorter draft on BACTpipe to share for general review and comments, unless anyone else feels like writing, or have another suggestion for how to do this.