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Build # 19643786736

Build Type

Pull #128

github

Committed by dpark01

Commit Message

Fix CLI argument parsing bugs and add metadata override parameters

This commit addresses all issues reported in #127:

## Fixed CLI Argument Parsing Bugs

Fixed TypeError in three CLI commands that used split_args=True with
incompatible main function signatures:
- illumina_metadata
- splitcode_demux_fastqs
- merge_demux_metrics

**Root cause:** Parsers used split_args=True but main functions expected
args object instead of **kwargs.

**Solution:** Embraced split_args=True pattern by:
- Removing wrapper functions (main_illumina_metadata, main_splitcode_demux_fastqs, main_merge_demux_metrics)
- Updating parsers to attach directly to underlying functions
- Moving logging from wrappers into actual functions

## Added Metadata Override Parameters

Added optional CLI parameters to splitcode_demux_fastqs:
- --flowcell_id: Override flowcell ID (default: extracted from FASTQ or RunInfo.xml)
- --run_date: Override run date in YYYY-MM-DD format (default: from RunInfo.xml)

These parameters allow users to override metadata without modifying RunInfo.xml,
useful for reprocessing data or synthetic test data.

## Test Coverage

Added parser-level regression tests for all three fixed commands:
- TestIlluminaMetadata.test_illumina_metadata_via_parser
- TestSplitcodeDemuxFastqs.test_splitcode_demux_fastqs_via_parser
- TestMergeDemuxMetrics.test_merge_demux_metrics_via_parser

All 106 illumina unit tests pass.

Closes #127

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

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

Pull Request Pull Request #128: Fix CLI argument parsing bugs and add metadata override parameters

Run Details

28 of 29 new or added lines in 1 file covered. (96.55%)

4187 of 6014 relevant lines covered (69.62%)

0.7 hits per line