docker-free kallisto collect

runs/kallisto_collect/run.cwl

 #!/usr/bin/env cwl-runner
+
 cwlVersion: v1.2
-class: Workflow
+class: CommandLineTool
+
 inputs:
-  in_kallisto_results:
-    type: Directory
-  in_metadata_file:
-    type: File
-  in_metadata_sample:
-    type: string
-  in_metadata_factor:
-    type: string
-  out_folder:
-    type: string
+- id: r_script
+  type: File
+  inputBinding:
+    position: 0
+- id: in_kallisto_results
+  type: Directory
+  inputBinding:
+    position: 1
+- id: in_metadata_file
+  type: File
+  inputBinding:
+    position: 2
+- id: in_metadata_sample
+  type: string
+  inputBinding:
+    position: 3
+- id: in_metadata_factor
+  type: string
+  inputBinding:
+    position: 4
+- id: out_folder
+  type: string
+  inputBinding:
+    position: 5
+
 outputs:
-  out_dir:
-    type:
-      type: array
-      items: Directory
-    outputSource: kallisto_collect/outdir
-steps:
-  kallisto_collect:
-    run: ../../workflows/kallisto_collect/workflow.cwl
-    in:
-      in_kallisto_results: in_kallisto_results
-      in_metadata_file: in_metadata_file
-      in_metadata_sample: in_metadata_sample
-      in_metadata_factor: in_metadata_factor
-      out_folder: out_folder
-    out: [outdir]
+- id: outdir
+  type:
+    type: array
+    items: Directory
+  outputBinding:
+    glob: $(runtime.outdir)/$(inputs.out_folder)
+
+baseCommand:
+- Rscript

runs/kallisto_collect/run.yml

 cores: 1
+r_script:
+  class: File
+  path: ../../workflows/kallisto_collect/kallisto_collect.R
 in_kallisto_results: 
   class: Directory
   path: ../kallisto_sleuth/out
 in_metadata_file: 
   class: File
-  path: ../merged_isa_metadata/merged_isa.tsv
+  path: ../merged_isa_metadata/out/merged_isa.tsv
 in_metadata_sample: "Sample.Name.2"
 in_metadata_factor: "Factor..Photosynthesis.mode."
 out_folder: out

workflows/kallisto_collect/kallisto_collect.R

 #!/usr/bin/env Rscript
 
-################################################
-#### CWL-independent tests
-################################################
-
-# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq_adrian/"
-# in_kallisto_results <- "runs/kallisto_quant/kallisto_results"
-# in_metadata_file <- "runs/merged_isa_metadata/merged_isa.tsv"
-# in_metadata_sample <- "Sample.Name.2"
-# in_metadata_factor <- "Factor..Photosynthesis.mode."
-# out_folder <- "runs/kallisto_collect"
-
 ################################################
 #### Load required library
 ################################################