diff --git a/workflows/no_CWL_yet/shiny_plots.Rmd b/workflows/no_CWL_yet/shiny_plots.Rmd
deleted file mode 100644
index 08e245ce822eb7f053f76ec7148c92dad73be27c..0000000000000000000000000000000000000000
--- a/workflows/no_CWL_yet/shiny_plots.Rmd
+++ /dev/null
@@ -1,106 +0,0 @@
----
-title: "Plot Talinum RNASeq data"
-output: html_document
-runtime: shiny
----
-
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-
-```
-
-
-```{r load_data, include=FALSE}
-
-# Load data
-
-load(file = "../runs/kallisto_sleuth/run2/05_shinyPrep.RData")
-
-```
-
-
-```{r plot_setup, message=TRUE, warning=TRUE, include=FALSE}
-
-# Setup plot environment 
-
-required.packages <- c('kableExtra', ## RMarkdown, 
-                      "shiny", "tidyverse", ## data loading and shaping
-                       "RColorBrewer" ## plotting
-                       )
-
-for(package in required.packages)
-{
-  print(package)
-  ## Check if package is installed. If not, install
-  if(!package %in% row.names(installed.packages()))
-    {install.packages(package, repos ="https://cran.uni-muenster.de/")}
-  ## Load package
-  library(package, character.only = T)
-}
-
-```
-
-
-```{r, eval = FALSE, echo = FALSE}
-
-
-# Non-interactive test
-
-current_selection <- sample(expression_data$target_id, 10)
-
-plot_set <- subset(expression_data, target_id %in% current_selection)
-
-ggplot(plot_set, aes(x = Photosynthesis.mode, y = tpm, group = Photosynthesis.mode)) + 
-    stat_summary(fun = 'mean', geom = 'bar') +
-    geom_point(size = 0.5) +
-    facet_wrap(~ target_id , scales = "free") + 
-    theme_minimal()
-
-```
-
-
-```{r shiny_part, echo=FALSE, message = F, error = FALSE, warning=FALSE}
-
-# Let it shine
-
-sidebarLayout(
-  
-  sidebarPanel(
-    
-    selectizeInput(multiple = T, "target", label = "Select Gene by target id",
-                   choices = available_genes, 
-                   selected = sample(available_genes, size = 3),
-                   options = list(delimiter = ' ',
-                   create = I("function(input, callback){return {value: input, text: input};}"))
-    ),
-    helpText("You can copy/paste target ids from excel")
-    
-  ),
-  
-  
-  mainPanel(
-    
-    renderPlot({
-      
-      
-      plot_set <- subset(expression_data, target_id %in% input$target)
-      
-      ## Facetted by gene only
-      
-      ggplot(plot_set, aes(x = Photosynthesis.mode, y = tpm)) + 
-        stat_summary(fun = 'mean', geom = 'bar') +
-        geom_point(size = 0.5) +
-        facet_wrap( ~ target_id, scales = "free") + 
-        theme_minimal() + 
-        theme(aspect.ratio = 1)
-      
-      
-    }),
-    
-    
-  )
-)
-  
-
-
-```
diff --git a/workflows/shiny_plots.Rmd b/workflows/shiny_plots.Rmd
new file mode 100644
index 0000000000000000000000000000000000000000..ecc2e1ef9878a1d09bb4dd5aa4efbfe0fc66fe0a
--- /dev/null
+++ b/workflows/shiny_plots.Rmd
@@ -0,0 +1,78 @@
+---
+title: "Plot Talinum RNASeq data"
+output: html_document
+runtime: shiny
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+
+```{r load_data, include=FALSE}
+
+# Load data
+
+load(file = "../runs/shiny_prep/shiny_prep.RData")
+```
+
+
+```{r load_libraries, message=TRUE, warning=TRUE, include=FALSE}
+# Load libraries
+
+library(kableExtra)
+library(shiny)
+library(RColorBrewer)
+library(tidyverse)
+```
+
+
+```{r, eval = FALSE, echo = FALSE}
+
+
+# Non-interactive test
+
+current_selection <- sample(expression_data$target_id, 10)
+
+plot_set <- subset(expression_data, target_id %in% current_selection)
+
+ggplot(plot_set, aes(x = condition, y = tpm, group = condition)) +
+  stat_summary(fun = "mean", geom = "bar") +
+  geom_point(size = 0.5) +
+  facet_wrap(~target_id, scales = "free") +
+  theme_minimal()
+```
+
+
+```{r shiny_part, echo=FALSE, message = F, error = FALSE, warning=FALSE}
+
+# Let it shine
+
+sidebarLayout(
+  sidebarPanel(
+    selectizeInput(
+      multiple = T, "target", label = "Select Gene by target id",
+      choices = available_genes,
+      selected = sample(available_genes, size = 3),
+      options = list(
+        delimiter = " ",
+        create = I("function(input, callback){return {value: input, text: input};}")
+      )
+    )
+  ),
+  mainPanel(
+    renderPlot({
+      plot_set <- subset(expression_data, target_id %in% input$target)
+
+      ## Facetted by gene only
+
+      ggplot(plot_set, aes(x = condition, y = tpm)) +
+        stat_summary(fun = "mean", geom = "bar") +
+        geom_point(size = 0.5) +
+        facet_wrap(~target_id, scales = "free") +
+        theme_minimal() +
+        theme(aspect.ratio = 1)
+    }),
+  )
+)
+```