fix: POC CWL

.gitignore

@@ -1 +1,3 @@
-data
+data
+.DS_Store
+output/*

README.md

@@ -16,3 +16,7 @@ To test, create `input` and `output` subfolders in the `data` directory. Create
 Re-Run: `docker-compose up --build`
 
 The testfile should be copied to the `data/output` directory.
+
+To run cwl file:
+
+`cwltool --outdir=data main.cwl job.yml`

job.yml

@@ -0,0 +1,7 @@
+# job.yml
+script:
+  class: File
+  path: main.py
+input_dir:
+  class: Directory
+  path: data/input

main.cwl

@@ -0,0 +1,34 @@
+cwlVersion: v1.2
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: hackathon/python
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: main.py
+        entry: $(inputs.script)
+      - entryname: data/input
+        entry: $(inputs.input_dir)
+      - entryname: data/output
+        entry: "$(null)"
+        writable: true
+  EnvVarRequirement:
+    envDef:
+      INPUT_DIR: "data/input"
+      OUTPUT_DIR: "data/output"
+
+inputs:
+  script:
+    type: File
+    doc: "The main Python script"
+
+  input_dir:
+    type: Directory
+    doc: "Input directory"
+
+outputs:
+  output_dir:
+    type: Directory
+    outputBinding:
+      glob: data/output