search

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
33 stars 15 forks source link

[Release] Update amrfinderplus database for June 2024 #511

Closed cimendes closed 1 week ago

kapsakcj commented 1 week ago

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

latest docker image is: staphb/ncbi-amrfinderplus:3.12.8-2024-05-02.2

needs to be tested first; then if all is well can copy docker image to our GAR and update the default in the WDL

kapsakcj commented 1 week ago

Testing here on a variety of species with theiaprok_illumina_pe v2.0.1: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/bf89ba48-b226-4be6-8243-fbce50d9a3eb

🤞

EDIT: ✅ workflows ran sucessfully.

kapsakcj commented 1 week ago

I want to note which organisms are not yet supported in our WDLs for organism-specific results from amrfinderplus.

Organisms available by the amrfinder --organism flag, but not yet implemented in WDL task/workflows (yet):

So basically what this means is that if these 3 species of bacteria are analyzed with TheiaProk (and this updated version of amrfinderplus v3.12.8; database v2024-05-02.2) then these samples will not have the --organism specific results and potentially miss some results

⚠️ P.S. I think there is supposed to be a space between the genus and species of Enterococcusfaecium on line 33 here. It depends on what string GAMBIT produces for this species: https://github.com/theiagen/public_health_bioinformatics/blob/39cc380840ba1ebff2bce2cb9cb5a1f3e9ee5479/tasks/gene_typing/drug_resistance/task_amrfinderplus.wdl#L33

kapsakcj commented 1 week ago

I won't update this part of the code as part of this PR (should be done after the 2.1.0 release), but wanted to note for whomever tackles this dev task in the future