broadinstitute / viral-core / 20463699069

70%

master: 70%

Pull #152

github

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>

38 of 39 new or added lines in 1 file covered. (97.44%)

4428 of 6325 relevant lines covered (70.01%)

0.7 hits per line