Hi there! I also plan to contribute to the scnanoseq project as a part of the hackathon. Could you please let me know which issues are not assigned and need more investigation? Thanks!

Awesome thanks! So at the moment we have the following: 1. Implementation of correct barcodes from BLAZE which @ryan has started to look at, but I think could be a task where team work would be beneficial if you prefer that. 2. We have a massive PR that just came in from @Luuk Harbers: https://github.com/nf-core/scnanoseq/pull/79 ; @g0bi may help with this, but this is very large and I think the more the better here to help us out in this review. 3. https://github.com/nf-core/scnanoseq/issues/94 -> strict syntax! After watching the intro video by @Phil Ewels, I felt guilty that I didn't add this to the hackathon roadmap in the website, so now it can certainly be if you would like to work on something that is totally unclaimed at the moment. We have a ton of other work in the workflow at the moment to do, so help with the syntax would be extremely appreciated. Let me know what you decide on (and if issue 94 is what you go with, I can tag it to the hackathon projects in GitHub). Thanks again for joining the event!

Thanks @Lara Ianov! #94 seems like a perfect task for nf beginners (I primarily use snakemake before😃)! I found this list of erros https://github.com/nf-core/strict-syntax-health/blob/main/lint_results/pipeline-results/scnanoseq_lint.md maybe I can contribute by fixing a few of these. So yes please assign #94 to me!

awesome! What is your github username?

YueYvetteHao

Done, thanks!

After watching the intro video by @Phil Ewels, I felt guilty that I didn't add this to the hackathon roadmap in the website

excellent My plan is working! 😆

@Yue Hao: if you have any updates to the strick syntax could you submit a PR to this fork and branch of scnanoseq? https://github.com/U-BDS/scnanoseq/tree/feature_strict_syntax

feature_strict_syntax

is the branch we just created in the forked repo - @Austyn Trull and I will start working on this soon and we can combine our efforts here before merging back to the main repo (the strict syntax timeline may affect our next release so we decided to prioritize it while we wait for some tests to run on other hackathon goals).

Got it, will do!

Protip (just did some strict syntax changes myself on a different pipeline): Github Copilot agents or Claude Code will fix all these in no time 😉

@Luuk Harbers agreed, Sequera AI CLI (note CLI specifically) helped me get through some changes much quicker!(Had to keep nf-core module patches in mind through and still lots to do and test given all the required changes)

Yea most of the work for me was module updates and changing input/output requirements from these updates