Extract filters to params

Author: ahmig

workflow/rules/vaf.smk

@@ -109,6 +109,10 @@ rule mask_tsv:
 rule filter_tsv:
     threads: 1
     conda: "../envs/renv.yaml"
+    params:
+        min_depth = 20,
+        min_alt_rv = 2,
+        min_alt_dp = 2,
     input: 
         tsv = OUTDIR/f"{OUTPUT_NAME}.masked.tsv",
         annotation = OUTDIR/"annotation.csv"

workflow/scripts/filter_tsv.R

@@ -12,24 +12,22 @@ log_threshold(INFO)
 # Read inputs
 data <- read_tsv(snakemake@input[["tsv"]])
 
-# Filtering criteria:
-# - P-value < 0.05
-# - Depth >= 20
-# - For SNP more than 2 reads in each strand
+# Filtering
 is.deletion <- str_detect(
   data$ALT,
   "^[A-Z]",
   negate = TRUE
 )
-inBothStrands <- data$ALT_RV > 2 & data$ALT_DP > 2
-Depth <- (data$ALT_RV + data$ALT_DP) >= 20
+strand.mask <- data$ALT_RV > snakemake@params$min_alt_rv &
+  data$ALT_DP > snakemake@params$min_alt_dp
+depth.mask <- (data$ALT_RV + data$ALT_DP) >= snakemake@params$min_depth
 
 log_info("Filtering variants")
 data <- filter(
   data,
   as.logical(PASS),
-  Depth,
-  inBothStrands | is.deletion
+  depth.mask,
+  strand.mask | is.deletion
 )
 
 log_info("Finding synonymous and non synonymous variants")