search

vsoch / scif

scientific filesystem: a filesystem organization for scientific software and metadata
https://sci-f.github.io/
Mozilla Public License 2.0
30 stars 13 forks source link

Nextflow-SCIF example : Possible solution #47

Closed saramonzon closed 5 years ago

saramonzon commented 5 years ago

Hi there, First of all, thank you for all your documentation and work, I have learned a lot this past couple of weeks!

I found that you tried to make an example with nextflow-scif. I have been working on a Nextflow-SCIF-Singularity implementation and I think I got it working with some "buts" but working.

If you want to take a look in case someone could use it is in this repo BU-ISCIII/nextflow-scif. Also, I have used some of your documentation for the README, I hope you don't mind. The goal is to create a template for easy development of new pipelines in our unit.

Please I would be very grateful if you could give me some feedback if you find the time! I am very new in containers and scif so surely there is something that could be improved!

Best regards Sara

vsoch commented 5 years ago

hey Sara, this is great! Do you want to move the repo (and still maintain ownership) over to scif, and/or add a link to the docs? I can definitely help with the buts if needed. I would much enjoy helping to make it nextflow ready, as I'm a big fan :)

saramonzon commented 5 years ago

Of course, there is no problem, do you mean you are going to fork the repo, or you want me to move it? I don't think I have done it before, but I can see how to do is if this is the case. Also you can use/link the documentation as you wish, a lot of that is obtained from your docs anyway xD. Yeah, I discovered all this container-nextflow universe just a couple of months ago and I am shaking up the whole bioinformatics unit infrastructure, it's awesome!

vsoch commented 5 years ago

Wicked!

I would suggest to either have it be a part of the nextflow set of repos, or I'd be happy to host it on scif! If the latter, I can also help to manage / update the code, and I would make you primary maintainer of it. Let me know what your preference is!

saramonzon commented 5 years ago

I think I prefer you to fork it and host it in scif first. Once you have it checked I can write to nextflow people and ask them if they want to add the repo to the list of nextflow repositories they have in nextflow-awesome. That way we have all bases covered XD.

vsoch commented 5 years ago

okay, definitely can do that! I'll fork and keep the sci-f master updated to yours. After I fork, is it all ready to "pretend I'm getting started using it" and I can submit a PR to your repo with feedback / suggestions?

saramonzon commented 5 years ago

That sounds great! I look forward to reading and including your suggestions and improvements! And yes, all should be just ready and working for anyone to use it, everytime I read it see something that could be improved, but that is the disease of this profession....

vsoch commented 5 years ago

haha, definitely! I'm going to fork and close the issue here. I'll open new issues on your board. I'm traveling now, but should still be able to work on this soon! :D