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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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Upgrade AMRFinderPlus to version 3.12.8 and DB to version 2024-01-31.1 #334

Closed cimendes closed 4 months ago

cimendes commented 5 months ago

:cool:

https://github.com/ncbi/amr/releases/tag/amrfinder_v3.12.8

kapsakcj commented 4 months ago

I just added a docker image for this to StaPH-B/docker-builds. Image will be available on dockerhub & quay momentarily.

We will need to copy the image over to our GAR & update the defaults in the WDL task (and at the same time, revisit the list of --organism options and update merlin_magic subwf, GAMBIT task (for assigning merlin_tag), and update the amrfinder WDL command block to accept the new organism options.

This issue is related to #129 which documents SOME of the new organisms, but we need to do a thorough check on the list of supported organisms from amrfinder. Check this docs page, but double check release notes to ensure we capture them all (sometimes the docs lag behind the software) https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus#--organism-option

kapsakcj commented 4 months ago

https://hub.docker.com/r/staphb/ncbi-amrfinderplus/tags

docker image name is staphb/ncbi-amrfinderplus:3.12.8-2024-01-31.1

sage-wright commented 4 months ago

Duplicated in #129, closing this one