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A new request to activate Zenodo for a pipeline ha...
# request-core
u
A new request to activate Zenodo for a pipeline has been made! • Pipeline name: cutandrun Core team will activate Zenodo for this pipeline. Please react to the message with ✅ when this is done. [This process is not automated] submitter: @Chris Cheshire
✅ 1
c
Hi all, we are trying to publish our pipeline but we need to edit our zenodo record for https://github.com/nf-core/cutandrun - trouble is I dont seem to be the owner of the record and I cant see it in my linked github area. Is there anyone in <!subteam^S016E36N7TQ> that could help? Perhaps they are the owners?! https://zenodo.org/records/10606804 (edited) Zenodo nf-core/cutandrun: nf-core/cutandrun v3.2.2 Iridium Ibis [3.2.2] - 2024-02-01 Enhancements Updated pipeline template to nf-core/tools 2.12. Added option to dump calculated scale factor values from the pipeline using --dump_scale_factors Added options to group IGV tracks by samplesheet group or by file type using --igv_sort_by_groups Fixes Fixed error that caused mismapping of IgG controls to their targets in certain samplesheet configurations.
m
What do you want to do?
c
Ideally become the owner of the record
im not sure why I am not
m
Usually zenodo record are made on release
So I'm a little against modifying them
c
We have to sync up and title and authors for JOSS submission
the author list is incorrect from a paper standpoint
its even got the nf-core bot in it 😂
m
Yeah it's automated from every commits
😆
c
Yeah the author list needs to be altered to fit the paper and the title cannot be the release title as this release will be tied to the paper
this is a JOSS requirement unfortunately
m
I'll see if it's possible to do anything to transfer ownership
c
thank you, or if someone is able to edit, thats also fine
which ever is easier really
m
@James Fellows Yates you have more practices with zenodo
j
I'm not able to edit it either. We need to find the person who created the repo initially
OR at least trasnferred it to nf-core, if it was outside originally
c
It was me i thought
j
Or maybe we need to find who activated the ZEnodo thingy?
c
it was me lol
i thought
but its not assigned to my account?!
im very confused
j
Oh so where we... we had a big confusion a while ago about it too
c
how did you find the owner, annoyingly they dont list it on zenodo
I published the 1.0.0 release which is the first one on zenodo
m
ok let me check
managed by another user too
c
oh for your pipelines?
j
What Iwas told by Zenodo support in Oct 2024: was read the link above
And
> As for the editing rights, they are with the person who owns the Github repository and enabled them on Zenodo. But you can grant editing access to different users by using our Share functionality. You can read more about it here: https://help.zenodo.org/docs/share/about/
Otherwise they are saying 'contact support'
So one other thing we can do is ask core team members to see if they have edit rights...
In the meantime...
c
I have raised a ticket yesterday, I just wanted to see if you guys knew anything
j
I think normally it was @Rike Hanssen @Phil Ewels and @Alex Peltzer other than myself and Maxime who were faffing with zenodo. Do any of you get an 'edit' button when looking here: https://zenodo.org/records/10606804
r
I locked myself out of Zenodo. Don't ask
😂 1
c
Anyone?
j
Phil and Alex are quite busy ATM afaik, and zneodo support are extremely overwhelmed - you will need to be patient either way - but in the meantime, maybe a silky hack: you could add a .zendo.json or citation.cff file and do another minor patch release with it correct. But is the syncing of Authors of the archive with the paper a request from an author? Because I personally do not Equate the two at all and thus it is not necessary
Or alternatively you just to a manual zendo archive of that release which is the publication archive
(the reason why I don't Equate the two: you can have people commit to the repo with tiny minor fixes that don't Equate to authorship)
c
Its a request from JOSS that the DOI matches as well as all the major information
👍 1
🫠 1
I can argue a point with the reviewers
j
I would give them those options
Because it will not be fast to fix because lots of broken stuff with zenodo
💯 1
👍 1
And we had a history of problems with this specific thing because of they. Way they pick up permissions and ownership
c
Thanks will try and put this to them!
👍 1
hey all -
Copy code
Dear Christopher,

While we cannot share the owner's personal details, they belong to the following organisation: @boehringer-ingelheim.com

To make an ownership transfer, we need to receive an e-mail from the original owner's Zenodo account e-mail address, with the new owner account in CC, stating the exact reasons for the transfer. Furthermore, we also need to receive a message reply from the new owner's Zenodo account email address accepting the transfer.

Best regards,
Rajesh
Does this ring any bells?
@James Fellows Yates
i recognise 
boehringer
Thats Sarek right?
p
That's probably @Alex Peltzer
a
Yeah thats me
I guess
What do you need @Chris Cheshire ?
I can login
(after 3 unsuccessful attempts)
c
Can you see an edit button?
that would indicate you are the owner haha
a
image.png
I am
c
awesome! we found you!
Would you mind initiating the record transfer to me please?
a
I added you via share button -> gave you permissions. Give it a try, should work now
Not possible to make you an owner, but giving you max permissions to work on the record
j
@Alex Peltzer can you also request adding it to the nf-core community?
In teh community section of the right hand bar
(then we might be able to edit it actually)
a
Ok 👌
c
Thanks all! I know have edit permissions
🎉 4
j
OK that's good to know @Alex Peltzer be prepared for future requests in teh future too 😅
😆 1
The best is we get everything under teh zenoedo nf-core org then we have more people with permissions
party this 2
a
Send it to community in this case too
If others pop up, just ping me here and I'll take care
🙏 1
j
I also confirm that nf-core core members who ar ein the Zenodo org can now edit everything too:
image.png
🎉 2
Thanks @Alex Peltzer!
m
Thanks @Alex Peltzer
p
Thanks @Alex Peltzer
a
🤠
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