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Ran 23 Dec 2025 02:55PM UTC

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Committed 23 Dec 2025 02:42PM UTC coverage: 70.008% (+0.3%) from 69.663%

Job # 20463699069.1

Build Type

Pull #152

github

Committed by

dpark01

Commit Message

Add metadata output to splitcode_demux_fastqs and make samplesheet optional in illumina_metadata

Task 1: Add --out_meta_by_sample and --out_meta_by_filename to splitcode_demux_fastqs
- Generates sample metadata JSONs with lane from FASTQ filename (fixes metadata/BAM mismatch)
- Works for both 2-barcode and 3-barcode demux paths
- Only includes samples matching the FASTQs outer barcodes

Task 2: Make samplesheet optional in illumina_metadata
- Samplesheet only required when sample metadata outputs are requested
- Derive index count from read structure (count B characters) instead of samplesheet
- Enables run-info-only mode for WDL workflows

Fixes metadata mismatch bug where illumina_metadata used lane=0 but
splitcode_demux_fastqs used actual lane from FASTQ filename.

Generated with Claude Code

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Pull Request Pull Request #152: Add metadata output to splitcode_demux_fastqs and make samplesheet optional

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