Add --allow-check-failures CLI flag to continue backup on validation failures

[Ulthran]

Motivation

• Allow running an archive job even when validation checks (file path vs header, file size, run consistency) fail so files can still be copied and MD5s generated.
• Prevent the CLI from aborting on non-critical validation issues while preserving visibility via warnings.
• Make the behavior configurable so operators can opt into lenient mode when needed.

Description

• Add an allow_check_failures parameter to backup_fastq with default False and propagate a new --allow-check-failures CLI flag to the function.
• Replace immediate ValueError raises for check_fp_vs_content, check_file_size, and run-consistency checks with collected result arrays so failures can be handled conditionally.
• Emit warnings.warn when checks fail and allow_check_failures is enabled, otherwise preserve the original ValueError behavior.
• Keep existing behavior for index-read warnings and sample sheet validation unchanged.

Testing

• No automated tests were run.

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Codex Task

[Copilot]

Pull request overview

This PR adds a configurable --allow-check-failures CLI flag that allows the backup process to continue when validation checks fail, converting fatal errors to warnings while still completing file archiving and MD5 generation.

Changes:

• Added allow_check_failures parameter to backup_fastq function with default False
• Refactored three validation checks (file path vs content, file size, and run consistency) to collect results in arrays and conditionally emit warnings instead of raising ValueError
• Added --allow-check-failures CLI argument that propagates the setting through to the backup function

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