remove cwl aux-tools

workflows/_aux-tools/collectFilesInDir.cwl

-cwlVersion: v1.2
-class: ExpressionTool
-doc: |
-  Takes Files (e.g. from a workflow step) and yields them in a desired directory.
-requirements:
-  - class: InlineJavascriptRequirement
-inputs:
-  files: File[]
-  destination: string
-expression: |
-  ${
-    return {"outDir": {
-      "class": "Directory", 
-      "basename": inputs.destination,
-      "listing": inputs.files
-    } };
-  }
-outputs:
-  outDir: Directory
\ No newline at end of file

workflows/kallisto/kallisto-workflow.cwl

@@ -57,7 +57,7 @@ steps:
       BootstrapSamples: BootstrapSamples
     out: [outFolder]
   collectResults:
-    run: ../_aux-tools/yield-dirInDestination.cwl
+    run: ./yield-dirInDestination.cwl
     scatter: inDir
     in:
       inDir: quant/outFolder

workflows/merge_isa_metadata/placeholder.cwl

-test
\ No newline at end of file