Repository for publication
How do we plan to publish the repository? Will we use the current gitlab repo or move to github?
The problem with the internal gitlab instance is that external users cannot open issues. The advantage of it is that we already have CI. Can we somehow combine them?
Activity
added Discuss Future Testing & CI/CD labels
changed milestone to %v0.2.0 release
The decision was that we tag and mirror to github but keep development on gitlab. @kanitz thoughts?
added To Do label
assigned to @gypas
I don't think it's a good idea to push directly from gitlab to zenodo, because we can't link back to gitlab (not publicly available). We can make it publicly available, but I would avoid this.
Solution: let's update the .gitlab ci to push the tags to a publicly available github repository (e.g. https://github.com/zavolanlab/zarp)
Regarding uploading, to zenodo the easiest way is to do it manually. I think using the API via CI is too much work (and a bit risky) as we have to adjust many different options and zenodo does not allow you to make too many changes afterward. So in case of mistakes, it will not be easy to fix.
Solution: Upload manually, but need the following information:
- Publication date
- Title
- **Authors (Family Name, Given Names, optionally ORCID)
- Description It would be nice here to have the github link
- Version
- Language (e.g. 'eng')
- Access right (e.g. Open access, Licence: Apache License 2.0)
- Grants It has options: Schweizerischer nationalfonds zur förderung der wissenschaftlichen forschung (CH) and Europen Commison (EU) which are relevant to us
ToDo:
- Update .gitlab ci to push the tags to -> https://github.com/zavolanlab/zarp @kanitz or @gypas
- @all provide the information needed (correct name and optionally ORCID). Especially @zavolan checks the grants part and the title and the description.
- Manually upload to zenodo (I can do that for every new version for this repo)
Example: Foivos Gypas, https://orcid.org/0000-0002-7233-8794
Dominik Burri https://orcid.org/0000-0002-8131-9309
I also have the following:
- Maciej Bak, https://orcid.org/0000-0003-1361-7301
- Mihaela Zavolan, https://orcid.org/0000-0002-8832-2041
- Alexander Kanitz, https://orcid.org/0000-0002-3468-0652
Edited by BIOPZ-Gypas FoivosAnastasiya Börsch, https://orcid.org/0000-0003-3392-5272
Maria Katsantoni, https://orcid.org/0000-0003-1961-0223
Short description of the software: Zarp is a snakemake-based workflow for the quality control and preliminary RNA-Seq library analysis developed by the Zavolan lab at the Biozentrum, University of Basel (https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/).
RNA-seq reads are pre-processed, aligned, and quantified with state-of-the-art tools to provide initial insights into the quality and composition of RNA-Seq libraries, cutting down the hands-on time for bioinformaticians and, most importantly, providing experimental scientists with entry points to exploring their data.
Christina J. Herrmann, https://orcid.org/0000-0003-1649-3463
Paula Iborra, https://orcid.org/0000-0003-0504-3029
@kanitz To finish the milestone %v0.2.0 release we need to upload things to zenodo.
To do so, we need to tag the version in master. Can you please do that (merge dev to master and tag) and I will do the zenodo upload.
Also, do we merge !73 (merged) before that or do we leave it for a later version? If not I can open a merge request (dev->master).
Edited by BIOPZ-Gypas FoivosMerged !73 (merged) as is and changed milestone on #136 (closed) to
v1.0.0. Will go ahead with tagging and merging.
