Rename extension to sbx_cenote_taker and drop VirSorter integration

[Ulthran]

Summary

• rename the extension to sbx_cenote_taker and update documentation
• remove VirSorter support and associated configuration, scripts, and environments
• ensure the workflow exclusively runs Cenote-Taker3 and reference the new environment assets

Testing

• not run (not requested)

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https://chatgpt.com/codex/tasks/task_e_68e51710b9b08323b599c7b42168c193

[Copilot]

Pull Request Overview

This PR renames the sbx_virus_id extension to sbx_cenote_taker and removes VirSorter2 support to focus exclusively on Cenote-Taker3 for viral identification. The changes streamline the workflow by eliminating the dual-tool approach and standardizing on a single viral identification method.

• Renamed extension from sbx_virus_id to sbx_cenote_taker throughout codebase
• Removed VirSorter2 integration including rules, scripts, environments, and configuration options
• Updated documentation to reflect Cenote-Taker3-only workflow

Reviewed Changes

Copilot reviewed 12 out of 13 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
scripts/filter_virsorter_contigs.py	Completely removed VirSorter filtering script
sbx_cenote_taker.smk	Main workflow file with extensive renaming and VirSorter rule removal
envs/virsorter_env.yml	Removed VirSorter conda environment definition
envs/virsorter_env.linux-64.pin.txt	Removed VirSorter environment pinned dependencies
envs/virsorter_env.Dockerfile	Removed VirSorter Docker environment
envs/spades_env.Dockerfile	Updated working directory to reflect new extension name
envs/sbx_virus_id.Dockerfile	Removed old Docker environment
envs/sbx_cenote_taker.yml	Renamed environment from sbx_virus_id to sbx_cenote_taker
envs/sbx_cenote_taker.Dockerfile	New Docker environment with updated naming
envs/cenote_taker_env.Dockerfile	Updated working directory to reflect new extension name
config.yml	Simplified configuration removing VirSorter options
README.md	Updated documentation for new extension name and Cenote-Taker3 focus

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