- Before, the expert configuration file had to be called
config_expert.txtand had to be positioned in the launching directory of the command line; it was then automatically detected and used; if such file was not present, then ksrates would use default expert parameters.
- To have a more flexible behaviour, now the user can define their own name/path for the expert configuration file: in both Nextflow and ksrates command lines this is done by adding parameter
--expertfollowed by the file name/path.
- Note that if
--expertis not given, the previous behaviour remains (
config_expert.txtautomatically detected in the launching folder and used; else default parameters used)
main.nf, processes that handle files from the reciprocally retained gene families now refer to such files with the most recent name format, which also states the top number of gene families and the ranking they come from, e.g.
extend_orthogroups.py, a checkpoint was added so that the diamond homology search between the focal species and the rec ret gene family database is also done when the diamond output file does already exists but it's empty (due to a failed earlier run).