Refactor

runs/kallisto_collect/kallisto_collect.yml

@@ -7,4 +7,4 @@ in_metadata_file:
   path: ../merged_isa_metadata/merged_isa.tsv
 in_metadata_sample: "Sample.Name.2"
 in_metadata_factor: "Factor..Photosynthesis.mode."
-out_folder: out
+out_folder: out
\ No newline at end of file

runs/kallisto_index/run.cwl

@@ -18,4 +18,4 @@ steps:
     in:
       in_genome_ref: in_genome_ref
       out_folder: out_folder
-    out: [outdir]
+    out: [outdir]
\ No newline at end of file

runs/merged_isa_metadata/merge_isa_metadata.yml

@@ -5,4 +5,4 @@ in_isa_study:
 in_isa_assay: 
   class: File
   path: ../../assays/Talinum_RNASeq_minimal/isa.assay.xlsx
-out_folder: out
+out_folder: out
\ No newline at end of file

workflows/kallisto_collect/workflow.cwl

 #!/usr/bin/env cwl-runner
-
 cwlVersion: v1.2.0-dev1
 class: CommandLineTool
 hints:
@@ -10,6 +9,8 @@ requirements:
     listing:
       - class: File
         location: kallisto_collect.R
+baseCommand:
+- Rscript
 arguments:
   - position: 0
     valueFrom: kallisto_collect.R
@@ -34,7 +35,6 @@ inputs:
   type: string
   inputBinding:
     position: 5
-
 outputs:
 - id: outdir
   type:
@@ -42,6 +42,3 @@ outputs:
     items: Directory
   outputBinding:
     glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
\ No newline at end of file

workflows/kallisto_index/workflow.cwl

 #!/usr/bin/env cwl-runner
-
 cwlVersion: v1.2.0-dev1
 class: CommandLineTool
 hints:
@@ -10,6 +9,8 @@ requirements:
     listing:
       - class: File
         location: kallisto_index.sh
+baseCommand:
+- bash
 arguments:
   - position: 0
     valueFrom: ./kallisto_index.sh
@@ -22,7 +23,6 @@ inputs:
   type: string
   inputBinding:
     position: 2
-
 outputs:
 - id: outdir
   type:
@@ -30,6 +30,3 @@ outputs:
     items: Directory
   outputBinding:
     glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- bash
\ No newline at end of file

workflows/kallisto_quant/workflow.cwl

 #!/usr/bin/env cwl-runner
-
 cwlVersion: v1.2.0-dev1
 class: CommandLineTool
 hints:

workflows/kallisto_sleuth/workflow.cwl

@@ -10,6 +10,8 @@ requirements:
     listing:
       - class: File
         location: kallisto_sleuth.R
+baseCommand:
+- Rscript
 arguments:
   - position: 0
     valueFrom: kallisto_sleuth.R
@@ -29,6 +31,3 @@ outputs:
     items: Directory
   outputBinding:
     glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
\ No newline at end of file

workflows/merge_isa_metadata/workflow.cwl

@@ -10,6 +10,8 @@ requirements:
     listing:
       - class: File
         location: merge_isa_metadata.R
+baseCommand:
+- Rscript
 arguments:
   - position: 0
     valueFrom: merge_isa_metadata.R
@@ -34,6 +36,3 @@ outputs:
     items: Directory
   outputBinding:
     glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript

workflows/shiny_prep/workflow.cwl

 #!/usr/bin/env cwl-runner
-
 cwlVersion: v1.2.0-dev1
 class: CommandLineTool
 hints:
@@ -10,6 +9,8 @@ requirements:
     listing:
       - class: File
         location: shiny_prep.R
+baseCommand:
+- Rscript
 arguments:
   - position: 0
     valueFrom: shiny_prep.R
@@ -22,7 +23,6 @@ inputs:
   type: File
   inputBinding:
     position: 2
-
 outputs:
 - id: outdir
   type:
@@ -30,6 +30,3 @@ outputs:
     items: Directory
   outputBinding:
     glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
\ No newline at end of file