Fix hamronization fargene input

[jasmezz]

This optimizes which hits from fARGene are summarized by hAMRonization: Before this PR, 2 files were in the hmmsearch output channel, but only one is required (the one starting with retrieved-genes-, as can be seen in the fARGene documentation:

Now, after the fargene module update, the ARG subworkflow pics the correct fargene output channel as input for hAMRonization and only the corrects show up in the final summary file (results/reports/hamronization_summarize/hamronization_combined_report.tsv tested and verified locally).

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c820d20

+| ✅ 333 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 2.0.0

❔ Tests ignored:

• actions_ci - actions_ci

✅ Tests passed:

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• nextflow_config - Config default value correct: params.arg_fargene_minorflength= 90
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• modules_config - ARGNORM_DEEPARG found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_TAXONOMY_COMBGC found in conf/modules.config and Nextflow scripts.
• 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 2024-08-15 12:11:58