Command paralogs-ks-multi is missing one argument when calling wgd_paralogs()

[Cecilia-Sensalari]

Command paralogs-ks-multi throws an error:

ksrates paralogs-ks-multi config_files/config_myspecies.txt
TypeError: wgd_paralogs() missing 1 required positional argument: 'test'

Cause

The click command calls wgd_paralogs() through:

wgd_paralogs(source, expert, n_threads, custom_recret_gfs, test)

but the defined wgd_paralogs function accepts an extra argument, parsed_homology_table, and therefore argument test remains undefined and throws the error:

def wgd_paralogs(config_file, expert_config_file, n_threads, custom_recret_gfs, parsed_homology_table, test)

Solution

This requires adding argument parsed_homology_table to the wgd_paralogs() call from command paralogs-ks-multi:

wgd_paralogs(source, expert, n_threads, custom_recret_gfs, parsed_homology_table, test)

Then it requires pushing a new container on Docker Hub. However, this is currently not possible due to the lack of paml4.9j.