diff --git a/runs/deseq2-run/README.md b/runs/deseq2-run/README.md
deleted file mode 100644
index f416fa74b81c27b40e1ede6cbaf308d5ba2e9287..0000000000000000000000000000000000000000
--- a/runs/deseq2-run/README.md
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
-
-```bash
-cd runs/deseq2-run
-```
-
-```bash
-cwltool ../../workflows/deseq2/deseq2.cwl job.yml
-```
diff --git a/runs/deseq2/run.cwl b/runs/deseq2/run.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..849cd989221e74fb6874efe6cc412166927a1847
--- /dev/null
+++ b/runs/deseq2/run.cwl
@@ -0,0 +1,24 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+
+inputs:
+  inKallistoResults: Directory
+  inMetadataFile: File
+  inMetadataSample: string
+  inMetadataFactorList: string[]
+
+steps:
+  deseq2:
+    run: ../../workflows/deseq2/workflow.cwl
+    in:
+      inKallistoResults: inKallistoResults
+      inMetadataFile: inMetadataFile
+      inMetadataSample: inMetadataSample
+      inMetadataFactorList: inMetadataFactorList
+    out: [output]
+
+outputs:
+  output: 
+    type: File[]
+    outputSource: deseq2/output
diff --git a/runs/deseq2-run/job.yml b/runs/deseq2/run.yml
similarity index 100%
rename from runs/deseq2-run/job.yml
rename to runs/deseq2/run.yml
diff --git a/workflows/deseq2/README.md b/workflows/deseq2/README.md
index 39cf2dcfacc76eeaee434d0f5d1abc07809fbe5d..4a64681c020e2dd6d7da19503fc7c82f39896bce 100644
--- a/workflows/deseq2/README.md
+++ b/workflows/deseq2/README.md
@@ -35,11 +35,6 @@ RScript deseq2.R "../../runs/kallisto/kallisto_results" "../../runs/merged_isa_m
 ```
 
 
-## Run CWL-wrapped script
-
-see [runs/deseq2-run](../../runs/deseq2-run)
-
-
 ## Multi-package containers
 
 - R and combinations of library dependencies are available as multi-package containers from [BioContainers](https://github.com/BioContainers/multi-package-containers)
diff --git a/workflows/deseq2/deseq2.cwl b/workflows/deseq2/workflow.cwl
similarity index 100%
rename from workflows/deseq2/deseq2.cwl
rename to workflows/deseq2/workflow.cwl