Refine subcommand pipelines

[Ulthran]

Summary

• adjust _run_paired_command to take a pipeline builder and reuse functools.partial when invoking it
• simplify each subcommand by directly passing its pipeline into the shared runner and extract a helper for trim-quality chaining

Testing

• python -m compileall src

---

https://chatgpt.com/codex/tasks/task_e_68dae3410b148323ab279fe828358255

[Copilot]

Pull Request Overview

This PR refactors the command structure to use a shared pipeline runner pattern with functools.partial for better code reuse and maintainability. The refactoring introduces a unified approach for handling paired FASTQ command processing with built-in statistics tracking.

• Introduces _run_paired_command function that handles common pipeline execution with input/output statistics
• Extracts _trim_quality_pipeline helper function to encapsulate the complex trimming logic
• Simplifies all subcommand functions to use the shared runner with partial function application

---

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}