diff --git a/R/qmd_template_parts.R b/R/qmd_template_parts.R
index 2ca5b00..91ffe00 100644
--- a/R/qmd_template_parts.R
+++ b/R/qmd_template_parts.R
@@ -3,7 +3,6 @@
 #' @param title Title for the report
 #' @param author Author for the report
 #' @param email Email of the author for the report
-#' @param ... Other parameters to set the yaml header
 #'
 #' @return opening_yaml string to be used to construct the report qmd
 #' @export
@@ -15,7 +14,13 @@
 template_yaml <- function(title = "RNA-Seq Report",
                           author = "Sameet",
                           email = "sameet.mehta@yale.edu",
-                          ...) {
+                          count_fn = "gene_count_matrix.csv",
+                          sample_fn = "sample-sheet.txt",
+                          contrast_fn = "contrasts.txt",
+                          metrics = NULL,
+                          outputdir = "rnaseq_report_outputs",
+                          thresh = 0.05
+                          ) {
   opening_yaml <- stringr::str_glue("
 ---
 title: \"{title}\"
@@ -41,7 +46,7 @@ params:
   contrasts_fn: null
   metrics: null
   outputs: \"{outputdir}\"
-  use_threshold: 0.05
+  use_threshold: {thresh}
 ---
   ")
   opening_yaml
@@ -74,6 +79,7 @@ We will import packages and functions.
 
 library(quartoReport)
 # use_thresh <- 0.05 # global threshold to use as alpha in the analysis
+if(!dir.exists(params$outputs)) dir.create(params$outputs)
 ```
 
 Please note that this package is currently under active development.
@@ -387,16 +393,16 @@ This is a deconstructed Venn Diagram that is much more interpretable.
 Upset plot for the data in this analysis is given in @fig_upset
 
 ```{{r}}
-#| label: fig_upset
+#| label: fig-upset
 #| fig-cap: UpSet plot with with significant genes seen across all the comparisons.
 
 upset_df <- make_upset_df(dds = dds, meta_df = meta_df,
                           contrasts_df = contrasts_df, thresh = params$use_threshold)
 upset_plot <- make_upset_plot(upset_df)
 ofn_upset <- file.path(params$outputs, \"upset-plot.pdf\")
-ggplot2::ggsave(filname = ofn_upset, device = \"pdf\", plot = upset_plot)
+ggplot2::ggsave(filename = ofn_upset, device = \"pdf\", plot = upset_plot)
 upset_plot
 ```
-In @fig_upset the number in the bars denotes number of genes satisfying that condition.
+In @fig-upset the number in the bars denotes number of genes satisfying that condition.
                                    ")
 }