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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
128 stars 36 forks source link

Add sourmash as a profiler (or similar) #112

Open jfy133 opened 2 years ago

jfy133 commented 2 years ago

Description of feature

Example workflow: https://taylorreiter.github.io/2022-07-28-From-raw-metagenome-reads-to-phyloseq-taxonomy-table-using-sourmash-gather-and-sourmash-taxonomy/

jfy133 commented 2 years ago

@Midnighter has already added some sourmash modules: https://github.com/nf-core/modules/blob/master/modules/sourmash/sketch/main.nf

vmikk commented 2 years ago

Sourmash module PR from Taylor Reiter: https://github.com/nf-core/modules/pull/2176 (not merged yet)

vmikk commented 2 years ago

For taxonomy profiling, we need a new module sourmash/gather (https://github.com/nf-core/modules/issues/2214)

vmikk commented 2 years ago

sourmash/gather should be working now (https://github.com/nf-core/modules/pull/2250). Now it's the turn for the sourmash/taxonomy module.

hkaspersen commented 1 year ago

Hello! I was wondering if you had a timeline for adding sourmash to Taxprofiler? I am very interested in trying it!

jfy133 commented 1 year ago

@vmikk is this still possible on your end, or would you like someone else to take over?

vmikk commented 1 year ago

Hello! I'm heavily engaged with my day job at the moment and unfortunately, I can't dedicate the necessary time to this project now. I apologize for any inconvenience caused by this delay. If quick completion is required, it would probably be more efficient if someone else could step in for now.

However, I've registered for the upcoming hackathon in Barcelona with the hope that it could provide an opportunity for me to finalize this task. I'm optimistic that the focused environment and collective energy at the event will allow me to make significant progress on this.

jfy133 commented 1 year ago

OK thanks for the update @vmikk ! We are about to release 1.1 anyway so I don't think sourmash will be fit in there in time.

If there are any taxprofiler devs in BCN maybe you can sit with them @vmikk and power through it! (I won't be there this year due to parental leave).

jfy133 commented 1 month ago

@vmikk I've removed you for now as I guess you're still very busy. Feel free to pick this up at a future date if you get time again @:)