ADD argNorm module to ARG subworkflow

[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.

In funcscan argNorm is part of the ARG screening subworkflow and it takes the hAMRonized outputs of deeparg, amrfinderplus, and abricate and normalizes them to the ARO.

[github-actions]

nf-core lint overall result: Passed ✅

Posted for pipeline commit 451cd52

+| ✅ 334 tests passed       |+
#| ❔   1 tests were ignored |#

❔ Tests ignored:

• actions_ci - actions_ci

✅ Tests passed:

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• nextflow_config - Config default value correct: params.arg_fargene_hmmmodel= class_a,class_b_1_2,class_b_3,class_c,class_d_1,class_d_2,qnr,tet_efflux,tet_rpg,tet_enzyme
• nextflow_config - Config default value correct: params.arg_fargene_minorflength= 90
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• base_config - AMPCOMBI2_PARSETABLES found in conf/base.config and Nextflow scripts.
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• modules_config - ARGNORM_DEEPARG found in conf/modules.config and Nextflow scripts.
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• modules_config - BGC_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
• modules_config - DRAMP_DOWNLOAD found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

• nf-core/tools version 2.14.1
• Run at 2024-07-24 20:37:29

[Vedanth-Ramji]

@nf-core-bot fix linting

[jfy133]

Mostly minor things, main thing is to update the snapshots for the other the tests, even if there is no changen in the output files

And then I think we are good to go!

[Darcy220606]

Very cool contribution. Thank you @Vedanth-Ramji 🎁

[jasmezz]

Only mini comments from my side, looks good overall!

[jasmezz]

Suggested change

	[argnorm](https://github.com/BigDataBiology/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](https://github.com/BigDataBiology/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 categorization of the drugs that antibiotic resistance genes confer resistance to.

[jfy133]

LGTM now thank you very much @Vedanth-Ramji !

Just waiting on the last snapshot update from Jasmin, and then the ✔️ from @Darcy220606 and good to go!

[Darcy220606]

LGTM atm!

[jasmezz]

Ready to merge once CI checks pass – go ahead 🚀