Handle lane-less Undetermined fastq files

[Ulthran]

Summary

• accept Undetermined fastqs without lane in filename
• ensure archived fastqs are renamed with L001 when missing
• test lane-less fastq parsing and backup

Testing

• pytest

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https://chatgpt.com/codex/tasks/task_e_689dfcb261788323b165309f4c2cb72e

[Copilot]

Pull Request Overview

This PR adds support for handling Illumina Undetermined FASTQ files that lack lane information in their filenames, ensuring they can be properly parsed and archived with appropriate lane identifiers.

• Extends FASTQ filename parsing to handle lane-less Undetermined files
• Updates archive logic to rename files with L001 when lane is missing from filename
• Adds comprehensive test coverage for both parsing and backup functionality

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
seqBackupLib/illumina.py	Adds regex pattern for lane-less Undetermined FASTQ files and fallback to header lane info
seqBackupLib/backup.py	Updates file path building and archiving to handle lane-less files with proper renaming
test/test_illumina.py	Tests parsing of lane-less FASTQ files and archive directory building
test/test_backup.py	Tests backup functionality for lane-less files including proper renaming

Comments suppressed due to low confidence (1)

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