align with spec: deseq2 (needs fix, missing dep)

runs/deseq2-run/README.md

-
-
-
-```bash
-cd runs/deseq2-run
-```
-
-```bash
-cwltool ../../workflows/deseq2/deseq2.cwl job.yml
-```

runs/deseq2/run.cwl

+#!/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

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)