From c735dc4f15fb16efad5baa747d11eabb97c9e82e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?=
 <m.alvarez.herrera@csic.es>
Date: Mon, 8 Jan 2024 10:22:24 +0100
Subject: [PATCH] Correct spelling mistakes and improve report style

---
 template.qmd              | 22 +++++++++++++---------
 workflow/rules/report.smk |  6 ++++++
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/template.qmd b/template.qmd
index 14bb402..d78b5bf 100644
--- a/template.qmd
+++ b/template.qmd
@@ -18,6 +18,9 @@ format:
 css: config/report.styles.css
 editor: visual
 params:
+  ufboot_reps: ""
+  shalrt_reps: ""
+  min_ivar_freq: ""
   workflow_version: ""
   div: ""
   freyja: ""
@@ -130,11 +133,12 @@ Samples in the X-axis are ordered chronologically, from more ancient to newer.](
 A maximum likelihood tree of the target and context samples has been
 built using [IQTREE](http://www.iqtree.org/).
 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).
+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 1000 support replicates of
-target datasets and their context samples. The clade that contains the target
+![Maximum-likelihood phylogeny with $`r ufboot_replicates`$ UFBoot
+and $`r shalrt_replicates`$ 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}
 
 ### Nucleotide diversity comparison
@@ -160,9 +164,9 @@ target samples.](`r params$div`){#fig-div}
 
 ### Number of polymorphic sites
 
-Sites with minor allele frequency > 0.05 are considered polymorphic.
+Sites with minor allele frequency $> `r min_ivar_freq`$ 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
+polymorphic sites has an $R^2$ of $`r nv.counts[["r2"]]`$ and a p-value of
 $`r nv.counts[["value"]]`$ (@fig-fig_cor_snp).
 
 ![Number of polymorphic sites along time. The
@@ -170,7 +174,7 @@ blue line shows the linear model fit.](`r params$fig_cor_snp`){#fig-fig_cor_snp}
 
 ### Description of intra-host nucleotide variants
 
-A total of `r n_SNV` different single nucleotide variants (SNV) and `r n_INDELS`
+A total of $`r n_SNV`$ different single nucleotide variants (SNV) and $`r n_INDELS`$
 insertions and deletions (indels) have been detected along the genome (@fig-SNV).
 
 ::: {.panel-tabset}
@@ -224,8 +228,8 @@ frequency-weighted distances.](`r params$tree`){#fig-tree}
 
 To estimate the substitution rate, root-to-tip distances measured on the previous
 tree (@fig-tree) have been correlated with time, obtaining a $R^2$ of
-**`r correlation`** and a p-value of $`r p_value_lm`$. The estimated substitution
-rate is **`r sub_rate`** substitutions per year (@fig-tempest).
+$`r correlation`$ and a p-value of $`r p_value_lm`$. The estimated substitution
+rate is $`r sub_rate`$ substitutions per year (@fig-tempest).
 
 ![Scatterplot depicting the relationship between root-to-tip
 distances and the number of days passed since the first sample. The red
diff --git a/workflow/rules/report.smk b/workflow/rules/report.smk
index e9ab0b2..3311730 100644
--- a/workflow/rules/report.smk
+++ b/workflow/rules/report.smk
@@ -190,6 +190,9 @@ rule report:
         omega_plot = report(rules.evo_plots.output.plot_omega)
     params:
         workflow_version = get_repo_version(BASE_PATH.as_posix(), __version__),
+        min_ivar_freq = config["VC"]["IVAR_FREQ"],
+        ufboot_reps = config["UFBOOT_REPS"],
+        shalrt_reps = config["SHALRT_REPS"],
         name = config["OUTPUT_NAME"]
     output:
         html = report(OUTDIR/f"{OUTPUT_NAME}.report.html")
@@ -200,6 +203,9 @@ rule report:
         set +o pipefail
         Rscript -e 'library(quarto)' -e \"quarto_render(input = '{input.qmd}',\
                                            execute_params=list( \
+                                                       ufboot_reps='{params.ufboot_reps}',\
+                                                       shalrt_reps='{params.shalrt_reps}',\
+                                                       min_ivar_freq='{params.min_ivar_freq}',\
                                                        workflow_version='{params.workflow_version}',\
                                                        div='{input.diversity}',\
                                                        freyja ='{input.freyja}',\