diff --git a/runs/kallisto_collect/kallisto_collect.yml b/runs/kallisto_collect/kallisto_collect.yml
index fa4ee11c61164f6e20956b206fe73a2ca1e9aaaf..78c3462bef0722ff7793c0947165af574e0ccf4b 100644
--- a/runs/kallisto_collect/kallisto_collect.yml
+++ b/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
\ No newline at end of file
+out_folder: out
diff --git a/runs/kallisto_index/run.cwl b/runs/kallisto_index/run.cwl
index efca83d8f86a30a9d59e30bcf250a8968b627deb..848b96d69b73dcd198332e1049d019633ef5c8c8 100644
--- a/runs/kallisto_index/run.cwl
+++ b/runs/kallisto_index/run.cwl
@@ -18,4 +18,4 @@ steps:
     in:
       in_genome_ref: in_genome_ref
       out_folder: out_folder
-    out: [outdir]
\ No newline at end of file
+    out: [outdir]
diff --git a/runs/merged_isa_metadata/merge_isa_metadata.yml b/runs/merged_isa_metadata/merge_isa_metadata.yml
index 4e4d2a1668ba45645c57f004285f966efbd225b6..675e868f6bd804759cda137e747c21294817ab45 100644
--- a/runs/merged_isa_metadata/merge_isa_metadata.yml
+++ b/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
\ No newline at end of file
+out_folder: out
diff --git a/workflows/kallisto_collect/workflow.cwl b/workflows/kallisto_collect/workflow.cwl
index 73f215d56aa8eea65018435aece4f365d456510a..a109fb0cb1d33cd5bfec67554e041adaa35ffd09 100644
--- a/workflows/kallisto_collect/workflow.cwl
+++ b/workflows/kallisto_collect/workflow.cwl
@@ -1,5 +1,4 @@
 #!/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
diff --git a/workflows/kallisto_index/workflow.cwl b/workflows/kallisto_index/workflow.cwl
index a91a17c6b4672f6ea484a0f7247a5e917e38a91d..f102e5c50562326df26659eb7f68da73d2504808 100644
--- a/workflows/kallisto_index/workflow.cwl
+++ b/workflows/kallisto_index/workflow.cwl
@@ -1,5 +1,4 @@
 #!/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
diff --git a/workflows/kallisto_quant/workflow.cwl b/workflows/kallisto_quant/workflow.cwl
index 5b45601a22367bdc63c4a027ef33bf15c3b6dda2..90aa9da3b9c65c9330edeb1c1f2b5a8d6bdb5b71 100644
--- a/workflows/kallisto_quant/workflow.cwl
+++ b/workflows/kallisto_quant/workflow.cwl
@@ -1,5 +1,4 @@
 #!/usr/bin/env cwl-runner
-
 cwlVersion: v1.2.0-dev1
 class: CommandLineTool
 hints:
diff --git a/workflows/kallisto_sleuth/workflow.cwl b/workflows/kallisto_sleuth/workflow.cwl
index 009ea5333f5ed49aa04e7e8aadf5e748b62e434e..ec2800ba2a9a7886f7e522d6db1538563a74b754 100644
--- a/workflows/kallisto_sleuth/workflow.cwl
+++ b/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
diff --git a/workflows/merge_isa_metadata/workflow.cwl b/workflows/merge_isa_metadata/workflow.cwl
index 436cc7d9fb37b2fb9a7f7f475bd0344fd6c01bbf..c6066ed7bd71d6a084afde5473f9151e8d657498 100644
--- a/workflows/merge_isa_metadata/workflow.cwl
+++ b/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
diff --git a/workflows/shiny_prep/workflow.cwl b/workflows/shiny_prep/workflow.cwl
index db3ff8b98e4f4cde7429b22c9a29b73afc56009f..4caf713393173d1bb20ca034fd2926c1e5301ac3 100644
--- a/workflows/shiny_prep/workflow.cwl
+++ b/workflows/shiny_prep/workflow.cwl
@@ -1,5 +1,4 @@
 #!/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