Added new runmode -m filter-orthology to filter BUSCO results according to settings in config.yaml
Samples are now filtered according to BUSCO completeness properly
Added new runmode -m filter-align to filter trimmed alignments according to settings in config.yaml
Trimmed alignments can now be filtered according to the number of parsimony informative sites.
BUSCO runmode is now called orthology (-m orthology) to have the possibility to user other methods for orthology inference in the future without having to change the name of the step.
Improved statistics output in report. Now it is more transparent what gets filtered when.
Update README to reflect these changes.
Update the phylociraptor script to reflect these changes.
Several small commits could be necessary in case problems show up with this new functionality.
This includes several changes to the pipeline:
Several small commits could be necessary in case problems show up with this new functionality.