refactor: update params names for clarity

Author: ahmig

workflow/rules/vaf.smk

@@ -308,8 +308,8 @@ rule pairwise_trajectory_correlation_data:
     params:
         cor_method=config["COR"]["METHOD"],
         cor_use="pairwise.complete.obs",
-        freq_amplitude_threshold=0.0,
-        n_threshold=0,
+        min_freq_amplitude=0.0,
+        min_unique_n=0,
     input:
         variants="<results>/<dataset>/variants.all_sites.tsv",
         metadata=config["METADATA"],

workflow/scripts/report/pairwise_trajectory_correlation_data.R

@@ -54,10 +54,10 @@ filtered <- all_variants_wider %>%
         # Drop empty
         if (length(clean_col) == 0) return(FALSE)
         # Unique values check
-        pass_unique <- length(unique(clean_col)) > snakemake@params$n_threshold
+        pass_unique <- length(unique(clean_col)) >= snakemake@params$min_unique_n
         # Amplitude check
         amplitude <- max(clean_col) - min(clean_col)
-        pass_amp <- amplitude >= snakemake@params$freq_amplitude_threshold
+        pass_amp <- amplitude >= snakemake@params$min_freq_amplitude
         return(pass_unique && pass_amp)
       }
     )