diff --git a/runs/shiny_prep/out/shiny_prep.RData b/runs/shiny/out/shiny_prep.RData
similarity index 100%
rename from runs/shiny_prep/out/shiny_prep.RData
rename to runs/shiny/out/shiny_prep.RData
diff --git a/runs/shiny/run.yml b/runs/shiny/run.yml
new file mode 100644
index 0000000000000000000000000000000000000000..98c88c6cfa62eae5e623887de1d03f76f12d2095
--- /dev/null
+++ b/runs/shiny/run.yml
@@ -0,0 +1,3 @@
+in_kallisto_df:
+ class: File
+ path: ../sleuth/out/kallisto_df.csv
\ No newline at end of file
diff --git a/runs/shiny_plots.Rmd b/runs/shiny_plots.Rmd
deleted file mode 100644
index 3a1e99cf680cdd3c67d2d5d55397db7e39147d13..0000000000000000000000000000000000000000
--- a/runs/shiny_plots.Rmd
+++ /dev/null
@@ -1,77 +0,0 @@
----
-title: "Plot Talinum RNASeq data"
-output: html_document
-runtime: shiny
----
-
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-```
-
-
-```{r load_data, include=FALSE}
-
-load(file = "../runs/shiny_prep/out/shiny_prep.RData")
-
-```
-
-
-```{r load_libraries, message=TRUE, warning=TRUE, include=FALSE}
-
-# Load libraries
-
-library(kableExtra)
-library(shiny)
-library(RColorBrewer)
-library(tidyverse)
-```
-
-
-```{r, eval = FALSE, echo = FALSE}
-
-# Non-interactive test
-
-current_selection <- sample(expression_data$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)
- }),
- )
-)
-```
diff --git a/runs/shiny_prep/run.cwl b/runs/shiny_prep/run.cwl
deleted file mode 100644
index aa7ea15dbeb66f345b610edc8c2ba3b0043d7851..0000000000000000000000000000000000000000
--- a/runs/shiny_prep/run.cwl
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.2
-class: CommandLineTool
-
-inputs:
-- id: r_script
- type: File
- inputBinding:
- position: 0
-- id: out_folder
- type: string
- inputBinding:
- position: 1
-- id: in_kallisto_df
- type: File
- inputBinding:
- position: 2
-
-outputs:
-- id: outdir
- type:
- type: array
- items: Directory
- outputBinding:
- glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
diff --git a/runs/shiny_prep/run.yml b/runs/shiny_prep/run.yml
deleted file mode 100644
index 8e7954b4766c5dabe9c6c4bac267ad186782abef..0000000000000000000000000000000000000000
--- a/runs/shiny_prep/run.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-cores: 1
-r_script:
- class: File
- path: ../../workflows/shiny_prep/shiny_prep.R
-in_kallisto_df:
- class: File
- path: ../sleuth/out/kallisto_df.csv
-out_folder: out
\ No newline at end of file
diff --git a/workflows/shiny/01-shiny-prep.R b/workflows/shiny/01-shiny-prep.R
new file mode 100644
index 0000000000000000000000000000000000000000..b8ae084aa7c21681fda025b464f5eb349187a8a5
--- /dev/null
+++ b/workflows/shiny/01-shiny-prep.R
@@ -0,0 +1,10 @@
+#!/usr/bin/env Rscript
+
+args <- commandArgs(trailingOnly = T)
+in_kallisto_df <- args[1]
+
+expression_data <- read.csv(file = in_kallisto_df)
+
+available_genes <- unique(expression_data$target_id)
+
+save(expression_data, available_genes, file = "01-shiny-prep.RData")
diff --git a/workflows/shiny/01-shiny-prep.RData b/workflows/shiny/01-shiny-prep.RData
new file mode 100644
index 0000000000000000000000000000000000000000..8750b371cd209ce904e08c21baac6b33a0be908a
Binary files /dev/null and b/workflows/shiny/01-shiny-prep.RData differ
diff --git a/workflows/shiny/01-shiny-prep.cwl b/workflows/shiny/01-shiny-prep.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..c79fdeec7154c8cf0638664ad6ffd3afaad75a77
--- /dev/null
+++ b/workflows/shiny/01-shiny-prep.cwl
@@ -0,0 +1,31 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+
+# hints:
+# DockerRequirement:
+# dockerPull:
+
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: 01-shiny-prep.R
+ entry:
+ $include: 01-shiny-prep.R
+ - class: NetworkAccess
+ networkAccess: true
+
+baseCommand: [Rscript, 01-shiny-prep.R]
+
+inputs:
+ in_kallisto_df:
+ type: File
+ inputBinding:
+ position: 1
+
+outputs:
+ outdir:
+ type: File
+ outputBinding:
+ glob: "01-shiny-prep.RData"
\ No newline at end of file
diff --git a/workflows/shiny/01-shiny-prep.yml b/workflows/shiny/01-shiny-prep.yml
new file mode 100644
index 0000000000000000000000000000000000000000..b2ec0e3b78cda23f9085bd0625f52ecaabc25345
--- /dev/null
+++ b/workflows/shiny/01-shiny-prep.yml
@@ -0,0 +1,3 @@
+in_kallisto_df:
+ class: File
+ path: ../../runs/sleuth/results/kallisto_df.csv
\ No newline at end of file
diff --git a/workflows/shiny/02-shiny-app.R b/workflows/shiny/02-shiny-app.R
new file mode 100644
index 0000000000000000000000000000000000000000..e2b3c8d56094dba4ebd5625a05d3878e22fd0c52
--- /dev/null
+++ b/workflows/shiny/02-shiny-app.R
@@ -0,0 +1,62 @@
+
+#!/usr/bin/env Rscript
+
+args <- commandArgs(trailingOnly = T)
+shiny_prep_data <- args[1]
+
+# Load libraries
+
+library(shiny)
+library(RColorBrewer)
+
+# Load data
+
+load(file = shiny_prep_data)
+
+# Design app
+
+ui <- fluidPage(
+
+ sidebarLayout(
+ sidebarPanel(
+ selectizeInput(
+ multiple = TRUE, "target", label = "Select Gene by target id",
+ selected = sample(available_genes, size = 3),
+ choices = NULL, # Start with no choices
+ options = list(
+ server = TRUE, # Enable server-side processing
+ delimiter = " ",
+ create = I("function(input, callback){return {value: input, text: input};}")
+ )
+ )
+ ),
+ mainPanel(
+ plotOutput("exPlot")
+ )
+ )
+)
+
+# Server logic
+server <- function(input, output, session) {
+
+ # Dynamically load the available genes
+ observe({
+ updateSelectizeInput(session, "target", choices = available_genes, server = TRUE)
+ })
+
+ output$exPlot <- renderPlot({
+ plot_set <- subset(expression_data, target_id %in% input$target)
+
+ # Facetted plot by gene
+ ggplot(plot_set, aes(x = condition, y = tpm)) +
+ stat_summary(fun = "mean", geom = "bar") +
+ geom_point(size = 0.5) +
+ facet_wrap(~target_id, scales = "free") +
+ theme_minimal() +
+ theme(aspect.ratio = 1)
+ })
+}
+
+# Launch app
+
+shinyApp(ui, server)
diff --git a/workflows/shiny_prep/shiny_prep.R b/workflows/shiny_prep/shiny_prep.R
deleted file mode 100644
index 804ad85db72c912c214f19b868e6073316524bab..0000000000000000000000000000000000000000
--- a/workflows/shiny_prep/shiny_prep.R
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env Rscript
-
-################################################
-#### Read arguments from CLI
-################################################
-
-args <- commandArgs(trailingOnly = T)
-
-out_folder <- args[1]
-in_kallisto_df <- args[2]
-
-################################################
-#### If it does not exist, create out dir
-################################################
-
-dir.create(out_folder, recursive = T, showWarnings = F)
-
-################################################
-#### Prep data for shiny app
-################################################
-
-expression_data <- read.csv(file = in_kallisto_df)
-
-available_genes <- unique(expression_data$target_id)
-
-save(expression_data, available_genes, file = paste(out_folder, 'shiny_prep.RData', sep = "/"))