Adding support for [email protected]

[llk578496]

Is your feature related to a problem?

The latest supporting model for --basecaller_cfg is [email protected].

Describe the solution you'd like

Is it possible to add the model [email protected] in the --basecaller_cfg? Thanks a lot.

Describe alternatives you've considered

Additional context

No response

[cjw85]

Hi @llk578496,

This is on our TODO list.

[ammaraziz]

I am getting a related issue. @cjw85 could please explain where the models are being retrieved from? The docker image of medaka or somewhere else? I am recieving this #104 error again. Trying to debug where/what is happening.

The model I am trying to run is [email protected] and also dna_r10.4.1_e8.2_400bps_hac

[cjw85]

@mattdmem

[ammaraziz]

@cjw85 @mattdmem Sorry to bug you guys, we've switched over to r10 but I'm struggling to get the pipeline to use the medaka r10 models. We're running the docker images in such a way that they can't access the internet.

I think I have identified the issue, the wf-artic docker image comes with only r941_min_hac_g507_model.tar.gz model.

Could the docker image please be updated to include r10 which is standard now?

Using the latest docker image:

docker run -it ontresearch/wf-artic:latest medaka tools resolve_model
/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/data/r941_min_hac_g507_model.tar.gz

using the 7month old one specified in the nextflow config:

docker run -it ontresearch/wf-artic:sha6e8c02f120faf92b4e61e1d0797d71210aaec20b medaka tools resolve_model
/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/data/r941_min_hac_g507_model.tar.gz

[julibeg]

Hi @llk578496 and @ammaraziz, the workflow and image have been updated. Could you please confirm if this fixes the issue? Thanks!

[ammaraziz]

Will test out this week or next. Thanks Julibeg!