Hi! Do you guys have decided what you want to implement for the pipeline? I have myself created a little genome annotation pipeline: https://github.com/OlivierCoen/genome_annotator Do you think we could sort of merge of different pipelines with the one existing?

We have kind of arrived at the conclusion that neither @Usman nor me have resources available to dedicate ourselves to maintaining an nf-core genomeannotator pipeline. We both have pipelines for genomeannotation, each with their own strengths which could probably merged into something even better. Largely that would be expanding usmans pipeline for long read support. Since both our pipelines are tailored towards plant genomes, we would have some steps (annotation of immunity genes) that might be plant specific. For reference the pipelines are: https://github.com/Plant-Food-Research-Open/genepal (@Usman) and https://github.com/nschan/nf-annotate (me).

Yes, thank you for the summary @Niklas Schandry Our pipelines are already public and usable. Olivier also has one now. The limited time that I have, I would like to spend on trying out the long read support in nf-annotate as well as explore other options for long reads. A unified nf-core pipeline is a worthy long term goal but it is an expensive endeavour in terms of time commitment.

I understand completely 😉 I'll try to revamp a bit this pipeline, because I think it's one of the key pipelines missing in nf-core. If you can validate from time to time my PRs, I would be more than grateful 🙂

I agree with you that it would be a valuable addition. For me it is really mainly the long-term commitment of maintaining the pipeline, which I am already struggling with for #C038XMTQWBT. I am happy to do reviews / discuss implementation

Yes #C038XMTQWBT is clearly a bit thing too. By the way, I will contact you quite soon for this pipeline because I made my own pipeline at https://github.com/OlivierCoen/EGCE-genomeassembler and I think it can bring interesting features to #C038XMTQWBT

Sure, sounds good, I am always happy to expand genomeassembler. Phasing and HiC scaffolding are missing and would be nice to have. My current endeavours for genomassembler are mainly focused on making it more useful for experimentation / comparisons of assembly strategies in single runs, not really adding new functionality.

I'm writing a message on the dedicated channel then 😉

It sounds to me like there is a transition happening. Please do not hesitate to ping me or any other core or maintainer member for help. and @oliviercoen don't hesitate to join #C04QR0T3G3H if you haven't already

Transition of maintainership? Sorry, though this was a thread in #C038XMTQWBT

what's the current status of #C0394F86LD9 then?

#C0394F86LD9 is as far as I can tell an abandoned pipeline

ok, then new maintainership

Hi @Maxime! I'd like to get ownership of this pipeline indeed. Another person in my lab is currently learning Nextflow / nf-core and would be willing to take maintainership in the middle run, but in the short run I'd like to lay the bases and revamp all this

@oliviercoen yeah, I just talked to Rémy, so I'm aware of the project

No, I think merging annotation and assembly into a single pipeline is going to be a pain

so everyone ok for @oliviercoen to lead here then?

Even a nightmare ^^and anyway most people want to do both separately

The only other people who have contemplated taking over this pipeline recently (to my knowledge) were @Usman and myself, and we both concluded that we cannot maintain this in addition to our current jobs. However, we also both have already existing annotation pipelines, with @Usman’s being more nf-core compliant than my own, and we would be happy to contribute to this pipeline.

I would definitively always strongly advise for collaboration

Sure, but once collaborators realize that the thing they thought would be easy will take longer than the 2 days they happen to have available it will fall back on the maintainer

I also made my own (simple yet generic) annotation pipeline, and so did Rémy, and a first step would be to merge them into a first version

My advice would be: start from scratch

that's exactly what I'd like to do

Unless you are already familiar with the current pipeline, figuring out what that person did where, and modernizing it will take longer and probably be more buggy than just doing your own thing. Especially since this was never released I do not see any advantage in sticking to whatever is there

Sounds like you're in alignment there. Please shout out if you need anything from me

Totally agree with you @Niklas Schandry My only concern was about nf-core policies, and if we could really "start from scratch". But if that's ok for @Maxime Garcia, then leeeet's gooo

We did that for some pipelines

I also did that for #C038XMTQWBT

yeah, go for it @oliviercoen, you have green light

Hi folks! Any news here? We have a related pipeline proposal: https://github.com/nf-core/proposals/issues/125

Hi! I've not had time to really work on it yet, but as soon #C07Q8HNU4FK first release is done, I should be able to dedicate some time to it ;)

Great, thanks! If you could write that in a comment on the issue for the record, that'd be great.