Skip to content

fix: extract flowcell ID, handle backslash paths, support 6-digit dates#81

Merged
simbig merged 4 commits intomasterfrom
fix-illumina-run-folder
Mar 11, 2026
Merged

fix: extract flowcell ID, handle backslash paths, support 6-digit dates#81
simbig merged 4 commits intomasterfrom
fix-illumina-run-folder

Conversation

@simbig
Copy link
Contributor

@simbig simbig commented Mar 11, 2026

Summary

Fixes IlluminaRunFolder from v6.5.0 to correctly handle real-world Illumina run folder formats:

  • Extract flowcell ID from raw segment using nemo's regex (000000000-AGKG7AGKG7)
  • Handle backslash pathsbasename() doesn't recognize \ as separator on Linux
  • Support 6-digit dates — older MiSeq runs use ymd format (e.g. 151231)
  • Use Carbon instead of CarbonImmutable — aligns with feat!: ban CarbonImmutable via PHPStan #80
  • Remove toString() and rawFlowcellSegment — no consumer, unclear semantics (YAGNI)

Test plan

  • 12 tests covering: MiSeq i100, MiSeq zero-prefix, NextSeq, Nano-FC, broken RFID, forward/backslash paths, error cases
  • PHPStan max level: 0 errors
  • Full test suite: 471 tests passing

🤖 Generated with Claude Code

simbig and others added 2 commits March 11, 2026 14:31
- Extract actual flowcell ID using nemo's regex (000000000-AGKG7 → AGKG7)
- Normalize backslashes so basename() works with Windows paths on Linux
- Support 6-digit dates (ymd format, e.g. 151231) alongside 8-digit (Ymd)
- Use Carbon instead of CarbonImmutable (aligns with #80)
- Remove unused toString() and rawFlowcellSegment (YAGNI)
- Add comprehensive test coverage for all Illumina run folder formats

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@simbig simbig force-pushed the fix-illumina-run-folder branch from d51e168 to 2d14332 Compare March 11, 2026 13:50
@simbig simbig requested a review from KingKong1213 March 11, 2026 14:01
Tests already document all format variants — no need to repeat
examples in docblocks. Remove internal GitLab reference.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@simbig simbig force-pushed the fix-illumina-run-folder branch from fb14f16 to 4af0d77 Compare March 11, 2026 14:06
@simbig simbig merged commit 830068d into master Mar 11, 2026
@simbig simbig deleted the fix-illumina-run-folder branch March 11, 2026 16:11
github-actions bot pushed a commit that referenced this pull request Mar 11, 2026
## [6.5.1](v6.5.0...v6.5.1) (2026-03-11)

### Bug Fixes

* extract flowcell ID, handle backslash paths, support 6-digit dates ([#81](#81)) ([830068d](830068d))
@github-actions
Copy link

🎉 This PR is included in version 6.5.1 🎉

The release is available on GitHub release

Your semantic-release bot 📦🚀

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

Development

Successfully merging this pull request may close these issues.

2 participants