Fix new template parameters

template.qmd

@@ -136,8 +136,8 @@ The target samples `r stats[["monophyly"]]` monophyletic. The clade
 that contains all the target samples is supported by a UFBoot score of
 $`r stats[["boot"]]`$% and a SH-aLRT score of $`r stats[["alrt"]]`$% (@fig-tree_ml).
 
-![Maximum-likelihood phylogeny with $`r ufboot_replicates`$ UFBoot
-and $`r shalrt_replicates`$ SH-aLRT support replicates of the
+![Maximum-likelihood phylogeny with $`r params$ufboot_replicates`$ UFBoot
+and $`r params$shalrt_replicates`$ SH-aLRT support replicates of the
 target dataset and its context samples. The clade that contains the target
 samples is squared in red.](`r params$tree_ml`){#fig-tree_ml}
 
@@ -164,7 +164,7 @@ target samples.](`r params$div`){#fig-div}
 
 ### Number of polymorphic sites
 
-Sites with minor allele frequency $> `r min_ivar_freq`$ are considered polymorphic.
+Sites with minor allele frequency $> `r params$min_ivar_freq`$ are considered polymorphic.
 The linear association between the collection date of the samples and the number of
 polymorphic sites has an $R^2$ of $`r nv.counts[["r2"]]`$ and a p-value of
 $`r nv.counts[["value"]]`$ (@fig-fig_cor_snp).