Restructure cwl

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