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nf-core / taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
https://nf-co.re/taxprofiler
MIT License
116 stars 33 forks source link

Allow hibf in ganon? #401

Open SannaAb opened 11 months ago

SannaAb commented 11 months ago

Description of feature

Thank you for a really nice tool.

I was going to try out ganon and was generating a database using their recommendation for refseq https://pirovc.github.io/ganon/default_databases/. 

ganon build --source refseq --organism-group archaea bacteria fungi viral --threads 48 --hibf --level species --db-prefix abfv_rs

When using it in taxprofiler i got errrors, I realized it was due to taxprofiler looking for ibf while i have hibf. I regenerated the database without the hibf but when testing it kept crashing due to depleted memory (running alone in a node with 512 GiB ram using an insilco sample of 6 species with 1M reads in total). Using the hibf version it runs fine.

Would it be possible to include hibf for ganon in taxprofiler?

jfy133 commented 11 months ago

Nope, no reason not to include that! We just need to update a search pattern in the Module :), should be easy

SannaAb commented 11 months ago

Awsome, when you looking into it can you also update ganon to the newest version? I was trying to use the tax flag but it seems it is not available for 1.5.1.

jfy133 commented 11 months ago

Yup! That's planned 👍

pirovc commented 10 months ago

Just a heads-up, a new ganon version (2.0) is planned to be out soon(ish) and there will be some parameter changes, where --hibf will vanish since it will be the default behavior (there will be a --ibf option then). I don't think this should stop this request but a newer ganon version may be out before you fix this.

sofstam commented 10 months ago

@pirovc Thanks for letting us know!

pirovc commented 9 months ago

ganon2 (ganon v2.0.0) is now released. The new behavior is to generate the .hibf by default with ganon build and ganon build-custom. The option to switch to the old filter type .ibf is now --filter-type ibf. Anyways, when using the database with ganon classify the extension does not matter, the tool will auto-detect the filter type. I hope that clarifies and simplifies the issue. There was also some other changes in parameters and output files https://github.com/pirovc/ganon/releases/tag/2.0.0

Would be great to have ganon2 in the taxprofiler, let me know if any help is needed.

jfy133 commented 9 months ago

Whoop! That's awesome, thanks @pirovc !

I will aim to update the nf-core module soonish (disclaimer: I'm on parental leave and as of this morning baby is sick, and Kita is shut for the rest of week 🙄 perfect combination). I'll ping you for review of the modules to make sure I've not missed any mandatory options 👍

Sorry for the slow progress on this @SannaAb will get there eventually

jfy133 commented 9 months ago

Oh and @pirovc always feel free to let us know if you feel like learning some nextflow or nf-core ;) we are happy to help you get involved 😉