[TheiaCoV_ONT] Update artic consensus docker image for more recent medaka models

[kapsakcj]

🆒

📌 Explain the Request

The docker image default we use in the artic consensus task is us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019-epi2me:latest

The medaka models included in this docker image do not include recent medaka models, here's what is included:

$ medaka --version
medaka 1.4.3

$ medaka tools list_models | tr ',' '\n'
Available: r103_fast_g507
 r103_fast_snp_g507
 r103_fast_variant_g507
 r103_hac_g507
 r103_hac_snp_g507
 r103_hac_variant_g507
 r103_min_high_g345
 r103_min_high_g360
 r103_prom_high_g360
 r103_prom_snp_g3210
 r103_prom_variant_g3210
 r103_sup_g507
 r103_sup_snp_g507
 r103_sup_variant_g507
 r10_min_high_g303
 r10_min_high_g340
 r941_min_fast_g303
 r941_min_fast_g507
 r941_min_fast_snp_g507
 r941_min_fast_variant_g507
 r941_min_hac_g507
 r941_min_hac_snp_g507
 r941_min_hac_variant_g507
 r941_min_high_g303
 r941_min_high_g330
 r941_min_high_g340_rle
 r941_min_high_g344
 r941_min_high_g351
 r941_min_high_g360
 r941_min_sup_g507
 r941_min_sup_snp_g507
 r941_min_sup_variant_g507
 r941_prom_fast_g303
 r941_prom_fast_g507
 r941_prom_fast_snp_g507
 r941_prom_fast_variant_g507
 r941_prom_hac_g507
 r941_prom_hac_snp_g507
 r941_prom_hac_variant_g507
 r941_prom_high_g303
 r941_prom_high_g330
 r941_prom_high_g344
 r941_prom_high_g360
 r941_prom_high_g4011
 r941_prom_snp_g303
 r941_prom_snp_g322
 r941_prom_snp_g360
 r941_prom_sup_g507
 r941_prom_sup_snp_g507
 r941_prom_sup_variant_g507
 r941_prom_variant_g303
 r941_prom_variant_g322
 r941_prom_variant_g360
Default consensus:  r941_min_hac_g507
Default snp:  r941_prom_hac_snp_g507
Default variant:  r941_prom_hac_variant_g507

For users sequencing on ONT, they are likely using Dorado with more up-to-date basecalling models and it would be good to having matching medaka models to be used for variant calling/consensus generation.

I am not sure if there are docker images available that we can use or not, likely not. We will have to be careful to ensure that the new docker image contains the same ARTIC workflow and a more recent version of medaka. Would be good to do some thorough testing with recently generated ONT data.

[kapsakcj]

perhaps wrap this nf workflow in a container and use it? Looks like the workflow has been nextflow-ified over time: https://github.com/epi2me-labs/wf-artic