[BUG]pyscenic ctx --no_pruning

[ken-chen-18]

From the SCENIC paper: "Only modules with significant motif enrichment of the correct upstream regulator are retained, and pruned to remove indirect target genes without motif support."

Does the --no_pruning option skip both of these steps? I have a dataset with a fair amount of non-coding RNA and other protein-coding RNA that may not be in the feather databases (although my gene names are formatted correctly). As a result, some modules are being skipped as they don't reach the 80% motif enrichment threshold. Is there a way to either lower this threshold or bypass the first step but perform the second (i.e. keep all modules, but remove indirect target genes within each module)?