Fix broken edge cases for unsufficient data

Author: ahmig

workflow/scripts/download_context.R

@@ -52,8 +52,8 @@ dates <- sample.metadata %>%
     pull(snakemake@params[["date_column"]]) %>%
     as.numeric
 window.quantile.offset <- (1 - snakemake@params[["date_window_span"]]) / 2
-min.date <- as_date(quantile(dates, window.quantile.offset))
-max.date <- as_date(quantile(dates, 1 - window.quantile.offset))
+min.date <- as_date(quantile(dates, window.quantile.offset, na.rm = TRUE))
+max.date <- as_date(quantile(dates, 1 - window.quantile.offset, na.rm = TRUE))
 padded.min.date <- min.date - snakemake@params[["date_window_paddding_days"]]
 padded.max.date <- max.date + snakemake@params[["date_window_paddding_days"]]
 print(glue("Time window (span={snakemake@params[['date_window_span']]}): {round(interval(min.date, max.date) / days(1))} days (from {min.date} to {max.date})"))

workflow/scripts/report/NV_description.R

@@ -448,15 +448,24 @@ n_indels <- vcf %>%
 
 n_snv <- length(unique(vcf$variant)) - n_indels
 model <- lm(n ~ CollectionDate, data = figur_SNP_table)
-cortest <- cor.test(figur_SNP_table$n, as.numeric(figur_SNP_table$CollectionDate))
+
+# Calculate correlation, if possible
+if (nrow(figur_SNP_table) > 2) {
+  p.cor <- cor.test(
+    figur_SNP_table$n,
+    as.numeric(figur_SNP_table$CollectionDate)
+  )$p.value
+} else {
+  p.cor <- NA
+}
 
 list(
   "INDELS" = n_indels,
   "SNV" = n_snv,
   "window" = snakemake@params[["window"]],
   "step"   = snakemake@params[["step"]],
   "r2"     = summary(model)$r.squared[[1]],
-  "value"  = ifelse(cortest$p.value < 0.001, "< 0.001", cortest$p.value)
+  "value"  = ifelse(p.cor < 0.001, "< 0.001", p.cor)
 ) %>%
   toJSON() %>%
   write(snakemake@output[["json"]])