dockerless merge isa

runs/merged_isa_metadata/run.cwl

 #!/usr/bin/env cwl-runner
 cwlVersion: v1.2
-class: Workflow
+class: CommandLineTool
 inputs:
-  in_isa_study:
-    type: File
-  in_isa_assay:
-    type: File
-  out_folder:
-    type: string
+- id: r_script
+  type: File
+  inputBinding:
+    position: 0
+- id: in_isa_study
+  type: File
+  inputBinding:
+    position: 1
+- id: in_isa_assay
+  type: File
+  inputBinding:
+    position: 2
+- id: out_folder
+  type: string
+  inputBinding:
+    position: 3
 outputs:
-  out_dir:
-    type:
-      type: array
-      items: Directory
-    outputSource: merge_isa_metadata/outdir
-steps:
-  merge_isa_metadata:
-    run: ../../workflows/merge_isa_metadata/workflow.cwl
-    in:
-      in_isa_study: in_isa_study
-      in_isa_assay: in_isa_assay
-      out_folder: out_folder
-    out: [outdir]
+- id: outdir
+  type:
+    type: array
+    items: Directory
+  outputBinding:
+    glob: $(runtime.outdir)/$(inputs.out_folder)
+
+baseCommand:
+- Rscript
\ No newline at end of file

runs/merged_isa_metadata/run.yml

 cores: 1
+r_script:
+  class: File
+  path: ../../workflows/merge_isa_metadata/merge_isa_metadata.R
 in_isa_study: 
   class: File
   path: ../../studies/TalinumFacultativeCAM/isa.study.xlsx

workflows/merge_isa_metadata/merge_isa_metadata.R

 #!/usr/bin/env Rscript
 
-################################################
-#### CWL-independent tests
-################################################
-
-# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq_adrian/"
-# in_isa_study <- "studies/TalinumFacultativeCAM/isa.study.xlsx:plant_growth"
-# in_isa_assay <- "assays/Talinum_RNASeq_minimal/isa.assay.xlsx:2EXT01_RNA:3ASY01_RNASeq"
-# out_folder <- "runs/merged_isa_metadata"
-
 ################################################
 #### Load required library
 ################################################

workflows/merge_isa_metadata/workflow.cwl

-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.2
-class: CommandLineTool
-hints:
-  DockerRequirement:
-    dockerPull: zimmera95/rnaseq:latest
-requirements:
-  - class: InitialWorkDirRequirement
-    listing:
-      - class: File
-        location: merge_isa_metadata.R
-baseCommand:
-- Rscript
-arguments:
-  - position: 0
-    valueFrom: merge_isa_metadata.R
-inputs:
-- id: in_isa_study
-  type: File
-  inputBinding:
-    position: 1
-- id: in_isa_assay
-  type: File
-  inputBinding:
-    position: 2
-- id: out_folder
-  type: string
-  inputBinding:
-    position: 3
-
-outputs:
-- id: outdir
-  type:
-    type: array
-    items: Directory
-  outputBinding:
-    glob: $(runtime.outdir)/$(inputs.out_folder)