cokelaer / quality_control / 24554786506

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Migrate quality_control pipeline to modern sequana standards

- Replace all wrapper: directives with manager.get_shell()/manager.get_run()
  (fastqc, bwa/build, bwa/align, fastp, rulegraph, dot2svg)
- Convert fastq_stats rules to inline run: blocks (Python, not pure shell)
- Replace pkg_resources with importlib.metadata in __init__.py
- Remove click_completion from main.py
- Add apptainers and cutadapt.tool_choice to config/schema
- Fix latent bugs: fastqc_trimmed wrong workdir, threads typo, missing container
- Add log redirect to copy_reference and compress_phix rules
- Update CI to micromamba v2 + micromamba-shell, Python 3.9-3.12
- Clean pyproject.toml deps, remove poetry.lock
- Update environment.yml, tools.txt (add graphviz)

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