ADD argNorm module

[Vedanth-Ramji]

argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.

argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.

argNorm takes the outputs of the hAMRonization module as well as ARG annotation tools (DeepARG, ARGs-OAP, ABRicate, ResFinder, and AMRFinderPlus) to normalize them to the antibiotic resistance ontology.

[muffato]

Hi @Vedanth-Ramji . The code looks fine (please fix the CI failure Details) but I have a question about the input channels you've defined for the module. The guidelines say that:

• "Non-file mandatory arguments (...) SHOULD be provided as value channels". I think that's the tool parameter 👍🏼
• "All non-mandatory command-line tool non-file arguments MUST be provided as a string via the $task.ext.args variable". I don't use argnorm myself but the documentation seems to indicate that --db and --hamronized are non-mandatory, and therefore shouldn't be promoted as input channels. Can you confirm ?

[Vedanth-Ramji]

Hi @muffato, yes, the tool parameter is mandatory.

argNorm doesn't always require the --db and --hamronized options, however, in some cases they are mandatory. For example, here, argNorm will throw an error if the '--db' option isn't provided. Also, if argNorm is taking inputs from the hAMRonization package, the --hamronized option is mandatory.

[Vedanth-Ramji]

@muffato thank you very much for the suggestions! I've gone ahead and implemented them now. Please let me know if you'd like me to change anything

[Vedanth-Ramji]

Thank you very much @muffato. I rebased the branch to be up to date with upstream. Is there anything else to be added before merging?

[muffato]

Thanks. I've kicked off the auto-merge, which will do a last CI run before merging.

[muffato]

All done 🚀