A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Anyone knows about <#C0493FQQZ3P> workflow? It seems abandoned? I found several problems (some serious bugs) but it seems that it's left on its own...

It can happen that pipelines become orphaned.
You are welcome to start contributing though, if you need someone to help review your PRs then we can find someone to do that.

Thanks! The code heavily uses deprecated syntax so doesn't work with nextflow 26+. That requires a massive refactoring. I can do that if it's ok.

That issue also blocks the CIs, any PR doesn't pass with latest-everything.

Basically the pipeline belongs to the community. If you wish to start to contribute, you are welcome

If you are willing to do it, go for it! You may want to post on the <#C0493FQQZ3P> channel, to see if anyone else is able to join your effort.

But to reiterate, please ping on <#CQY2U5QU9> to get someone to look at your PRs, and we can support you getting the pipeline up to date. A template merge will likely help with some of the strict syntax, although the most recent <https://github.com/nf-core/rnasplice/pull/175|automated template PR> is 3.3.1? <@UQZG2UCF3>?

<https://nfcore.slack.com/archives/C0493FQQZ3P/p1752236863876149>

I've been able to update to the latest template, but there's still a lot of work to do to for the deprecated syntax. I'll also match the latest versions of nf-core modules and subworkflows.

I'd highly recommend doing discrete PRs (apart from the template merge), they are earlier to review and merge

Now it seems that linting is fine, the major work is now to fix the pipeline. I'll open follow up PRs.

Please focus on getting a version that is running on CI, then do any actual fixes to logic.
I see that <https://github.com/nf-core/rnasplice/pull/195/> incorporates a lot of module/subworkflow updates, that is an example of things that are easier to review separately.

yes, many of these were necessary to pass the linting.