diff --git a/runs/.gitkeep b/runs/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/workflows/_aux-tools/collectFilesInDir.cwl b/workflows/_aux-tools/collectFilesInDir.cwl
deleted file mode 100644
index f8d411fe571e1a22a08e23a6dc472cd5ac1c25d1..0000000000000000000000000000000000000000
--- a/workflows/_aux-tools/collectFilesInDir.cwl
+++ /dev/null
@@ -1,19 +0,0 @@
-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
diff --git a/workflows/kallisto/kallisto-workflow.cwl b/workflows/kallisto/kallisto-workflow.cwl
index e7f0350801fb853d1dc23a029c2d2f161e00b1c1..1d020e1110afc46d500e96eef07a1f7282164219 100644
--- a/workflows/kallisto/kallisto-workflow.cwl
+++ b/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
diff --git a/workflows/_aux-tools/yield-dirInDestination.cwl b/workflows/kallisto/yield-dirInDestination.cwl
similarity index 100%
rename from workflows/_aux-tools/yield-dirInDestination.cwl
rename to workflows/kallisto/yield-dirInDestination.cwl
diff --git a/workflows/merge_isa_metadata/placeholder.cwl b/workflows/merge_isa_metadata/placeholder.cwl
deleted file mode 100644
index 30d74d258442c7c65512eafab474568dd706c430..0000000000000000000000000000000000000000
--- a/workflows/merge_isa_metadata/placeholder.cwl
+++ /dev/null
@@ -1 +0,0 @@
-test
\ No newline at end of file