snakemakelib
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percyfal
Snakemake library for bioinformatics programs, with a focus on next-generation sequencing
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 ```
Data output is now collected via rules, making heavy use of pandas. This functionality should also be present in standalone scripts, along the following lines: ``` collect_results.py --samples SAMPLE1 SAMPLE2......
Current rule is not adapted to using "file:" syntax as options -b and -B duplicate the values of 'threeprime' and 'fiveprime'