feat: enable user to configure CLI params per rule
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- Snakefile 404 additions, 90 deletionsSnakefile
- pipeline_documentation.md 56 additions, 52 deletionspipeline_documentation.md
- tests/input_files/config.mutliple_lanes.yml 2 additions, 1 deletiontests/input_files/config.mutliple_lanes.yml
- tests/input_files/config.yaml 2 additions, 1 deletiontests/input_files/config.yaml
- tests/input_files/rule_config.yaml 148 additions, 0 deletionstests/input_files/rule_config.yaml
- workflow/rules/paired_end.snakefile.smk 100 additions, 28 deletionsworkflow/rules/paired_end.snakefile.smk
- workflow/rules/single_end.snakefile.smk 95 additions, 24 deletionsworkflow/rules/single_end.snakefile.smk
- workflow/scripts/zarp_multiqc_config.py 3 additions, 3 deletionsworkflow/scripts/zarp_multiqc_config.py
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