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nf-core / bacass

Simple bacterial assembly and annotation pipeline
https://nf-co.re/bacass
MIT License
60 stars 41 forks source link

Add flye to nf-core/bacass #115

Open lborcard opened 6 months ago

d4straub commented 6 months ago

It would be great to have flye in here, but I do want to highlight that currently a template update would be really necessary.

Daniel-VM commented 6 months ago

I'm on it, @d4straub! 👍🏾 I'm encountering a bit of trouble getting the latest template update to work in nf-core/bacass.

Daniel-VM commented 6 months ago

In addition, I would like to mention that we need to consider implementing Flye because it can already be accessed through the Dragonflye module, which is already implemented but in the development branch. I have to make a release ASAP 🏃🏾 .

lborcard commented 6 months ago

Ok thanks @Daniel-VM , I am now working on adding Flye, it's my first time contributing to nf-core, I was looking for guidance as waht is necessary to do.

Daniel-VM commented 6 months ago

Awesome @lborcard. We have other interesting approaches in mind re: #57 . For example, improving assembled genomes by adding a genome rotation step. We proposed here cyclator or dnaapler or both.

Should we try them? (Feel free to open a new issue to cover this genome rotation task 😃 )

lborcard commented 6 months ago

Awesome @lborcard. We have other interesting approaches in mind re: #57 . For example, improving assembled genomes by adding a genome rotation step. We proposed here cyclator or dnaapler or both.

Should we try them? (Feel free to open a new issue to cover this genome rotation task 😃 )

It seems that dnaapler is more recent and recently maintained but I don't have experience with either of these tools.

lborcard commented 6 months ago

So dnaapler/cyclator would take the output of Dragonflye? is there a module for either of these tools?

jenmuell commented 6 months ago

Dragonflye is already present as module

Daniel-VM commented 6 months ago

So dnaapler/cyclator would take the output of Dragonflye? is there a module for either of these tools?

I think so. I have never tryed yet, but it is likely that dnaapler takes the assembled genome *.fasta emmited by any assembler used in nf-core bacass (dragonflye, unicycler, miniasm, ...).

lborcard commented 6 months ago

I can work on a dnaapler module if that would help?

Daniel-VM commented 6 months ago

Sure 💯 . Please add a git issue for dnaapler implementation ;).

lborcard commented 6 months ago

i added it to the list