Summary

• Adds new SAV module for parsing Illumina RunInfo.xml and RunParameters.xml files
• Provides basic run information display (run ID, flowcell, instrument, cycles, dates, etc.)
• Adds general stats columns for key run metrics
• Includes sav_extra plugin hook to allow external plugins to add InterOp-based visualizations

Architecture

Following the pattern established in #3376, this module keeps heavy dependencies external:

• Core SAV module (this PR): Lightweight XML parsing with no external dependencies
• MultiQC_SAV plugin (Convert to hook-based plugin architecture MultiQC_SAV#7): InterOp-based visualizations requiring interop library

The sav_extra hook allows the external plugin to inject additional sections when installed:

if "sav_extra" in plugin_hooks.hook_functions:
    for hook_fn in plugin_hooks.hook_functions["sav_extra"]:
        hook_fn(self)

Features

• Parses RunInfo.xml for run structure (reads, lanes, cycles, flowcell info)
• Parses RunParameters.xml for additional metadata (application version, RTA version, chemistry)
• Shows run information section with key details
• Adds general stats for quick overview

Test plan

• Tested with NextSeq 500 run data
• Verified file pattern matching with shared: true for RunInfo.xml (shared with bclconvert)
• Run pytest test suite
• Test with various Illumina platforms (MiSeq, HiSeq, NovaSeq)

Related: MultiQC/MultiQC_SAV#7 (plugin providing InterOp visualizations)

Resolves #1431

🤖 Generated with Claude Code