Hi all, I'm working on adding Parabricks GPU accelerated minimap2 to the scnanoseq pipeline this hackathon. I'll also be adding some subworkflow and pipeline level testing since I don't see any already in the repo.

Great, thank you!

@Lara Ianov @Austyn Trull I added you both as reviewers for my PRs since they're both passing the CI runners and ready to merge. Definitely need to add pipeline tests if Austyn has that PR. Happy to help there, because GPUs on the CI runners can get tricky.

Awesome thank you!

Thank you so much. I'm glad I was able to help. I'm looking forward to being an scnanoseq contributor!

Thank you so much Gary, we really appreciate your support here. We are excited to run your addition to scnanoseq in the GPUs we have at UAB.

Yes once it's all integrated, I would love to know what impact it has on your runtimes with real data.

We will certainly report back!

Hey yall! Wanted to check in and see how the pipeline work is going and offer any help that I can.

Hi @Gary Burnett, Thanks for checking-in. We have been split between a few different workflows, but @Austyn Trull is getting back on track for this one. Here are the updates and plans so you are in the loop (some of which we hope to be finished prior to the Summit, but we shall see [depends how it goes...]): 1. We will be updating IsoQuant once more to implement their latest enhancements - the work so far is in our fork and branch: https://github.com/U-BDS/scnanoseq/tree/feature_isoquant_upgrade 2. Austyn has added most of the nf-tests - https://github.com/U-BDS/scnanoseq/tree/feature_nftest ; If you spot anything missing here let us know! 3. I started working on the strick syntax conversion but was not able to finish it during the time I could devote to it: https://github.com/U-BDS/scnanoseq/tree/feature_strict_syntax ; the critical piece missing here is updating the main workflow file including dealing with the version channels which are now being handled through topics. We need to get through 1-3 above, before we implement your GPU work. The challenge here is actually merging all this as well. The plan now will be to 1. Finish the stick syntax conversion (nf-core has a timeline on this so we need to prioritize), and then go from there on the other merged. We will need to test all this pieces of course to ensure we didn't break anything critical. Once we finish the above, we will do a release to that users can benefit from IsoQuant enhancements right away, and then we will immediately move to reviewing and merging your PR. After testing, we will then do another release with just this feature. How can you help? I think that depends on wheather you feel like tackling any of the above with us 🙂 We would certainly welcome the help but we know the scope here is wide. Austyn is out today, but I will let him also give you his thoughts once he is back in tomorrow.

Thank you for the update, Lara! I will probably be more helpful when you start to merge the GPU related PRs. I will be at the summit in person if either of you plan on attending.

Excellent, I will be sure to ping you here when we get there 🙂 I will be in the summit as well so let's touch base there.

Thank you much for the update and congratulations on the new release!