trying to fix use of R with CWL

runs/kallisto/README.md

 # Kallisto Workflow
 
-## Executing individual steps
+## Executing the multi-step workflow
 
 ```bash
 cd runs/kallisto/

runs/kallisto_collect/README.md

+
+
+```bash
+cd runs/kallisto_collect/
+cwltool ../../workflows/kallisto_collect/kallisto_collect.cwl run.yml > $(date +"%Y-%m-%d_%H-%M").log 2>&1 &
+```

runs/kallisto_collect/run.yml

-cores: 1
-r_script:
-  class: File
-  path: ../../workflows/kallisto_collect/kallisto_collect.R
-in_kallisto_results: 
+in_kallisto_results:
   class: Directory
-  path: ../kallisto_sleuth/out
+  path: ../runs/kallisto/kallisto_results
 in_metadata_file: 
   class: File
   path: ../merged_isa_metadata/out/merged_isa.tsv

workflows/kallisto_collect/kallisto_collect.R

@@ -4,9 +4,14 @@
 #### Load required library
 ################################################
 
-library(sleuth)
-library(tidyverse)
-library(jsonlite)
+if(!"BiocManager" %in% row.names(installed.packages())){install.packages('BiocManager')}
+
+if(!"sleuth" %in% row.names(installed.packages())){
+  BiocManager::install('pachterlab/sleuth')
+}
+if(!"tidyverse" %in% row.names(installed.packages())){install.packages("tidyverse")}
+if(!"openxlsx" %in% row.names(installed.packages())){install.packages("openxlsx")}
+if(!"jsonlite" %in% row.names(installed.packages())){install.packages("jsonlite")}
 
 ################################################
 #### Read arguments from CLI

runs/kallisto_collect/run.cwl → workflows/kallisto_collect/kallisto_collect.cwl

@@ -3,11 +3,19 @@
 cwlVersion: v1.2
 class: CommandLineTool
 
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entryname: kallisto_collect.R
+        entry:
+          $include: kallisto_collect.R
+  - class: NetworkAccess
+    networkAccess: true
+
+baseCommand: [Rscript, kallisto_collect.R]
+
 inputs:
-- id: r_script
-  type: File
-  inputBinding:
-    position: 0
+
 - id: in_kallisto_results
   type: Directory
   inputBinding:
@@ -36,6 +44,3 @@ outputs:
     items: Directory
   outputBinding:
     glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript