Add extra check messages

workflow/scripts/report/NV_description.R

@@ -160,6 +160,7 @@ npc <- read_csv(snakemake@params[["nsp"]]) %>%
 ## SUMMARY FIGURE FOR WHOLE GENOME
 log_info("Plotting summary figure for whole genome")
 
+log_info("Checking table size")
 if (nrow(vcf) == 0) {
   log_warn("Whole-genome VCF has no rows")
   vcf <- empty_vcf
@@ -314,13 +315,14 @@ window_plot_spike <- window %>%
     x = ""
     )
 
+log_info("Checking table size")
 if (nrow(vcf_spike) == 0) {
-  log_warn("Spike VCF has no rows")
-  log_warn(vcf_spike$REGION)
+  log_warn("Spike VCF has no rows!")
   vcf_spike <- empty_vcf
-  log_warn(vcf_spike$NV_class)
 }
 
+log_info(vcf_spike$NV_class)
+
 variants_spike <- vcf_spike %>%
   ggplot() +
   aes(
@@ -385,6 +387,7 @@ figur_SNP_table <- vcf_snp %>%
     ) %>%
   ungroup()
 
+log_info("Checking table size")
 if (nrow(figur_SNP_table) == 0) {
   log_warn("Filtered SNP table has no rows")
   figur_SNP_table <- empty_vcf