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MaestSi / UMInator

A Nextflow pipeline for generating consensus sequences from Nanopore reads tagged with UMIs
GNU General Public License v3.0
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medaka model #7

Closed nic-ong closed 2 months ago

nic-ong commented 2 months ago

Hi, thank you for creating this UMInator tool - I've had trouble with Karst's longread_umi pipeline and that sadly hasn't been maintained/updated since 2020, while yours has worked really well.

Could I please make a request though? The latest medaka version release is now v1.12.0, and I would like to use the more recent dorado basecaller models (sup v5.0) on my R10.4.1 nanopore data with your UMInator tool. Unfortunately, I noticed that the medaka package bundled in your docker image (maestsi/uminator) at the moment is v1.9.1, which only includes up to the v4.2.0 basecaller models e.g. r1041_e82_400bps_sup_v4.2.0.

If you could push out an updated docker image with the latest medaka version whenever you have the bandwidth, that would be much appreciated! :)

Thank you very much! Cheers, nic-ong

MaestSi commented 2 months ago

Hi, you should be able to find the updated docker image on DockerHub. Please let me know if you are able to download it and run the pipeline. Best, SM

nic-ong commented 2 months ago

Hi, thanks for your incredible responsiveness! I could pull your updated docker image with medaka v1.12.0 and ran UMInator successfully with a more recent medaka model r1041_e82_400bps_sup_v4.3.0! Much appreciated!