broadinstitute / viral-core / 20446705465

70%

master: 70%

Pull #151

github

Add --append_run_id parameter to illumina_metadata command

Fixes #150. The illumina_metadata command now supports --append_run_id
to append flowcell ID and lane to library IDs in metadata output,
matching the behavior of illumina_demux and splitcode_demux_fastqs.

This ensures metadata JSON 'run' fields match BAM filenames when
demux commands use --append_run_id, preventing 0% match rates in
downstream tasks that try to match metadata to BAM files.

Changes:
- Add --append_run_id argument to parser_illumina_metadata
- Add append_run_id parameter to illumina_metadata function
- Build run_id_str from flowcell and lane, pass to SampleSheet
- Add unit tests for the new functionality

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

5 of 5 new or added lines in 1 file covered. (100.0%)

4392 of 6288 relevant lines covered (69.85%)

0.7 hits per line