cokelaer / mapper / 26785806710

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github

Add optional FastQC on raw reads (--do-fastqc); bump to 1.5.0

- 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)

3 of 3 new or added lines in 1 file covered. (100.0%)

59 of 73 relevant lines covered (80.82%)

1.62 hits per line