Initial commit
* snakemakelib/__init__.py: Remove Apache license
* snakemakelib/ext/__init__.py: Add
- Add rules and workflows
- add make2snakemake.py
- add module
Modify lots of rules
* rules/bio/ngs/settings.rules: add configuration variables to define configuration dictionary key names
* rules/bio/ngs/tools/gatk.rules: port biomake rules
* rules/utils.rules: add docstring
* rules/bio/ngs/align/bwa.rules: Update key strings
* rules/bio/ngs/genetics/plink.rules: Define rules
* rules/bio/ngs/settings.rules: Update key strings
* rules/bio/ngs/tools/bedtools.rules: Update docstring
* rules/bio/ngs/tools/gatk.rules: Make use of variables for config dict keys
* rules/settings.rules: Add
* rules/bio/ngs/tools/bedtools.rules: Add configuration string variables
* rules/utils.rules: Update configuration rules. Add rules to print rule docs.
Add snakemakelib/variables.py to enforce consistent naming of config dictionary keys