Per Unneberg
Per Unneberg
Add label region_{LABEL} to region-based analyses, e.g. region_chr1
bokeh dependency: currently some plots rely on bokehutils but I would like to replace with bokeh charts.
E.g. import index, annotation in bio.ngs.align.settings as these are used for _all_ alignment programs. This settings file would import bio.ngs.settings.
Currently, DEFAULT_RULES are defined in each rule settings file. In some cases, e.g. workflows, it would be preferable to set rules that are required for full functionality.
Complementary to config['samples'], e.g. exclude_samples
Add sphinx rst templates for sphinx-based rule: ``` sphinx-build -C -D master_doc=index -D extensions=bokeh.sphinxext.bokeh_plot report/ html ```