Update Slurm benchmarking script for paired FASTQ inputs

[Ulthran]

Summary

• hardcode a paired FASTQ input list and derive matching OUT_ outputs
• submit Slurm jobs across thread/compression combinations while collecting job IDs

Testing

• python -m compileall scripts/benchmark_slurm.py

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https://chatgpt.com/codex/tasks/task_e_68f92aaf07e483239cc602c4c14e3c27

[Copilot]

Pull Request Overview

This PR introduces a Slurm benchmarking script for heyfastq that handles paired FASTQ inputs. The script automates the submission of multiple benchmarking jobs with different thread counts and compression levels.

• Hardcoded paired FASTQ input paths with automatic output path derivation
• Automated Slurm job submission across configurable thread and compression combinations
• Job ID collection and tracking from sbatch submissions

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[Copilot]

The hardcoded placeholder paths '/path/to/input_R1.fastq.gz' and '/path/to/input_R2.fastq.gz' should be replaced with actual paths or made configurable through command-line arguments or environment variables to make the script usable without modification.

[Copilot]

[nitpick] The generator expressions are unpacked directly into command_parts. Convert these to lists using list() to avoid potential issues with generator exhaustion and improve code clarity: *[str(path) for path in inputs] and *[str(path) for path in outputs].

Suggested change

	*(str(path) for path in inputs),
	"--output",
	*(str(path) for path in outputs),
	*[str(path) for path in inputs],
	"--output",
	*[str(path) for path in outputs],