Changes to captus extract, all related to clustering:
- The clustering workflow logic has been improved. For example, if the clustering input file is found it can be reused if the clustering parameters change in a new run. Extraction of clusters is performed if a valid target file is found in the clustering directory instead of just skipping it if clustering was previously run.
- A new option
--exlcude_sampleshas been added, these samples are not used for clustering, but the targets derived from the clustering of the rest of samples are still extracted from the excluded samples. - Changed
easy-clusteras the default algorithm for MMSeqs when clustering withcaptus extract