bug: Fix TRNA_COLLECT and COMBINE_ANNOTATIONS for large # inputs

[madeline-scyphers]

rewrite TRNA_COLLECT to use pandas vectorized functions instead of embedded for loops to significantly streamline creation of collected_trnas.tsv with large # of inputs. Now instead of taking hours or days, it will run in seconds or minutes.

rewrite COMBINTE_ANNOTATIONS to take directories of inputs instead of a cli list of files so that when you have thousands and thousands of mags or assemblies you don't run into your system's ARG_MAX.

[Copilot]

Pull Request Overview

This PR optimizes performance for large datasets by replacing inefficient Python loops with vectorized operations in TRNA_COLLECT and modifying COMBINE_ANNOTATIONS to accept directories instead of file lists to avoid ARG_MAX limitations.

• Rewrites TRNA_COLLECT to use pandas vectorized functions instead of embedded for loops for faster processing
• Changes COMBINE_ANNOTATIONS to accept directories of inputs instead of CLI file lists to handle thousands of MAGs/assemblies
• Removes nf-boost plugin from Nextflow configuration

Reviewed Changes

Copilot reviewed 4 out of 6 changed files in this pull request and generated 2 comments.

File	Description
nextflow.config	Removes unused nf-boost plugin
modules/local/collect_rna/trna_scan.nf	Simplifies error handling by removing NULL file writing
modules/local/collect_rna/trna_collect.nf	Replaces Python loops with shell AWK command and external script
modules/local/annotate/combine_annotations.nf	Updates to use directory-based inputs instead of file lists

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[Copilot]

Typo in comment: 'excape' should be 'escape'.

Suggested change

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	# we use backslash here to escape nf/groovy interpolation and use bash {# feature