align with spec: isaSampleToRawData

runs/isaSampleToRawDataSeq-run/README.md

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

runs/isaSampleToRawDataSeq/run.cwl

+cwlVersion: v1.2
+class: Workflow
+
+inputs:
+  arcPath: Directory 
+  assayName: string
+  startingNodeNum: int
+  outName: string
+
+steps:
+  isaSampleToRawDataSeq:
+    run: ../../workflows/isaSampleToRawDataSeq/workflow.cwl
+    in:
+      arcPath: arcPath
+      assayName: assayName
+      startingNodeNum: startingNodeNum
+      outName: outName
+    out: [output]
+
+outputs:
+  output: 
+    type: File[]
+    outputSource: isaSampleToRawDataSeq/output
+

workflows/isaSampleToRawDataSeq/README.md

-
-
-```bash
-
-dotnet fsi isaSampleToRawDataSeq.fsx ../../ Talinum_RNASeq_minimal 1 rnaseq-samples
-
-```

workflows/isaSampleToRawDataSeq/isaSampleToRawDataSeq.cwl → workflows/isaSampleToRawDataSeq/workflow.cwl

 cwlVersion: v1.2
 class: CommandLineTool
+
+doc: |
+  Run script with `dotnet fsi isaSampleToRawDataSeq.fsx ../../ Talinum_RNASeq_minimal 1 rnaseq-samples`
+
 hints:
   DockerRequirement:
     dockerPull: mcr.microsoft.com/dotnet/sdk:8.0