convert shiny to single-step cwl

runs/shiny/run.cwl

+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: Workflow
+
+inputs:
+  in_kallisto_df: File
+  exp_factor: string
+
+steps:
+  run_shiny:
+    run: ../../workflows/shiny/workflow.cwl
+    in:
+      in_kallisto_df: in_kallisto_df
+      exp_factor: exp_factor
+    out: []
+
+outputs: []

runs/shiny/run.yml

 in_kallisto_df: 
   class: File
-  path: ../sleuth/out/kallisto_df.csv
+  path: ../../runs/sleuth/results/kallisto_df.csv
\ No newline at end of file
+exp_factor: "Factor..Photosynthesis.mode."
\ No newline at end of file

workflows/shiny/01-shiny-prep.R

-#!/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")

workflows/shiny/01-shiny-prep.yml

-in_kallisto_df: 
-  class: File
-  path: ../../runs/sleuth/results/kallisto_df.csv
\ No newline at end of file

workflows/shiny/02-shiny-app.R → workflows/shiny/shiny-app.R

-
 #!/usr/bin/env Rscript
 
-args <- commandArgs(trailingOnly = T)
-shiny_prep_data <- args[1]
-
 # Load libraries
 
 library(shiny)
 library(RColorBrewer)
+library(ggplot2)
+
+# CLI arguments
+
+args <- commandArgs(trailingOnly = T)
+in_kallisto_df <- args[1]
+exp_factor <- args[2]
 
 # Load data
 
-load(file = shiny_prep_data)
+expression_data <- read.csv(file = in_kallisto_df)
+available_genes <- unique(expression_data$target_id)
+
+expression_data$condition = expression_data[,exp_factor]
 
 # Design app
 

workflows/shiny/01-shiny-prep.cwl → workflows/shiny/workflow.cwl

@@ -10,22 +10,22 @@ class: CommandLineTool
 requirements:
   - class: InitialWorkDirRequirement
     listing:
-      - entryname: 01-shiny-prep.R
+      - entryname: shiny-app.R
         entry:
-          $include: 01-shiny-prep.R
+          $include: shiny-app.R
   - class: NetworkAccess
     networkAccess: true
 
-baseCommand: [Rscript, 01-shiny-prep.R]
+baseCommand: [Rscript, shiny-app.R]
 
 inputs:
   in_kallisto_df:
     type: File
     inputBinding:
       position: 1
+  exp_factor:
+    type: string
+    inputBinding:
+      position: 2
 
-outputs:
-  outdir:
+outputs: []
\ No newline at end of file
-    type: File
-    outputBinding:
-      glob: "01-shiny-prep.RData"
\ No newline at end of file