Add optional FastQC on raw reads (--do-fastqc); bump to 1.5.0#33
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- new --do-fastqc CLI flag enables FastQC on raw input reads - fastqc rule + config/schema block, output folded into MultiQC report - tools.txt, environment.yml, README docs updated - test_full covers --do-fastqc; new test_standalone_script_fastqc - README: fix `sh mapper.sh` -> `bash mapper.sh`, drop stale fastqc note Note: bundles pre-existing uncommitted bwa_split fixes in mapper.rules. 🤖 Generated with [Claude Code](https://claude.com/claude-code)
Not up to standards ⛔🔴 Issues
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| Category | Results |
|---|---|
| Security | 2 high |
🟢 Metrics 0 complexity · 0 duplication
Metric Results Complexity 0 Duplication 0
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sh mapper.sh->bash mapper.sh, drop stale fastqc noteNote: bundles pre-existing uncommitted bwa_split fixes in mapper.rules.