broadinstitute / viral-core / 19769443323

69%

master: 72%

Pull #140

github

Add append_run_id support to splitcode_demux_fastqs

Fixes #139: Output BAM filenames now use proper library name format
for SRA submission compatibility.

Changes:
- Add --append_run_id flag to include flowcell.lane in BAM filenames
- Fix bug: BAM filenames now use sample_library_id (from 'run' column)
  instead of sample_name, ensuring library_id_per_sample is included
- Without flag: {sample}.l{library_id}.bam (e.g., H2O.l1.bam)
- With flag: {sample}.l{library_id}.{flowcell}.{lane}.bam
  (e.g., H2O.l1.HKWJJDSX7.1.bam)

This affects both 2-barcode and 3-barcode code paths. The SampleSheet
class already builds the correct 'run' field format, so the fix
leverages existing functionality rather than duplicating logic.

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

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

10 of 11 new or added lines in 1 file covered. (90.91%)

4182 of 6043 relevant lines covered (69.2%)

0.69 hits per line