From e286f029b2f1b9074830d578eb078efb380b4f2b Mon Sep 17 00:00:00 2001
From: Edmore Moyo <etmoyo@gmail.com>
Date: Tue, 15 Apr 2025 16:56:30 -0400
Subject: [PATCH 1/4] initial changes

---
 .gitignore |  3 ++-
 job.yml    | 11 +++++++++++
 main.cwl   | 36 ++++++++++++++++++++++++++++++++++++
 3 files changed, 49 insertions(+), 1 deletion(-)
 create mode 100644 job.yml
 create mode 100644 main.cwl

diff --git a/.gitignore b/.gitignore
index 6320cd2..7106392 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
-data
\ No newline at end of file
+data
+.DS_Store
diff --git a/job.yml b/job.yml
new file mode 100644
index 0000000..079de1f
--- /dev/null
+++ b/job.yml
@@ -0,0 +1,11 @@
+script:
+  class: File
+  path: ./main.py
+
+input_dir:
+  class: Directory
+  path: ./data/input
+
+output_dir:
+  class: Directory
+  path: ./data/output
diff --git a/main.cwl b/main.cwl
new file mode 100644
index 0000000..fb915a8
--- /dev/null
+++ b/main.cwl
@@ -0,0 +1,36 @@
+cwlVersion: v1.2
+class: CommandLineTool
+
+baseCommand: ["python", "main.py"]
+
+requirements:
+  DockerRequirement:
+    dockerPull: python:3.11
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: main.py
+        entry: $(inputs.script)
+
+inputs:
+  script:
+    type: File
+    inputBinding: {}
+    doc: "The main Python script"
+
+  input_dir:
+    type: Directory
+    inputBinding:
+      prefix: "data/input"
+      separate: false
+
+  output_dir:
+    type: Directory
+    inputBinding:
+      prefix: "data/output"
+      separate: false
+
+outputs:
+  output_data:
+    type: Directory
+    outputBinding:
+      glob: data/output

From 12fa41fdef48badd20219d9b078ce68d207c19a0 Mon Sep 17 00:00:00 2001
From: Edmore Moyo <etmoyo@gmail.com>
Date: Tue, 15 Apr 2025 19:15:06 -0400
Subject: [PATCH 2/4] refactors

---
 .gitignore |  1 +
 job.yml    | 10 +++-------
 main.cwl   | 26 +++++++++++++-------------
 3 files changed, 17 insertions(+), 20 deletions(-)

diff --git a/.gitignore b/.gitignore
index 7106392..044922b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 data
 .DS_Store
+output/*
diff --git a/job.yml b/job.yml
index 079de1f..d336d6b 100644
--- a/job.yml
+++ b/job.yml
@@ -1,11 +1,7 @@
+# job.yml
 script:
   class: File
-  path: ./main.py
-
+  path: main.py
 input_dir:
   class: Directory
-  path: ./data/input
-
-output_dir:
-  class: Directory
-  path: ./data/output
+  path: data/input
\ No newline at end of file
diff --git a/main.cwl b/main.cwl
index fb915a8..451b5ed 100644
--- a/main.cwl
+++ b/main.cwl
@@ -1,36 +1,36 @@
 cwlVersion: v1.2
 class: CommandLineTool
 
-baseCommand: ["python", "main.py"]
+baseCommand: ["python3.13", "main.py"]
 
 requirements:
   DockerRequirement:
-    dockerPull: python:3.11
+    dockerPull: python:3.13.1
   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
-    inputBinding: {}
     doc: "The main Python script"
 
   input_dir:
     type: Directory
-    inputBinding:
-      prefix: "data/input"
-      separate: false
-
-  output_dir:
-    type: Directory
-    inputBinding:
-      prefix: "data/output"
-      separate: false
+    doc: "Input directory"
 
 outputs:
   output_data:
     type: Directory
     outputBinding:
-      glob: data/output
+      glob: data/output
\ No newline at end of file

From 67e9d117c55bde1085d5f049c9e4ef7740eade65 Mon Sep 17 00:00:00 2001
From: Edmore Moyo <etmoyo@gmail.com>
Date: Wed, 16 Apr 2025 13:45:03 -0400
Subject: [PATCH 3/4] update to use pre-built docker image

---
 main.cwl | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/main.cwl b/main.cwl
index 451b5ed..8882716 100644
--- a/main.cwl
+++ b/main.cwl
@@ -1,11 +1,9 @@
 cwlVersion: v1.2
 class: CommandLineTool
 
-baseCommand: ["python3.13", "main.py"]
-
 requirements:
   DockerRequirement:
-    dockerPull: python:3.13.1
+    dockerPull: hackathon/python
   InitialWorkDirRequirement:
     listing:
       - entryname: main.py
@@ -30,7 +28,7 @@ inputs:
     doc: "Input directory"
 
 outputs:
-  output_data:
+  output_dir:
     type: Directory
     outputBinding:
       glob: data/output
\ No newline at end of file

From 7e00988d900b74a78ce7a956ff2075400abe4237 Mon Sep 17 00:00:00 2001
From: Edmore Moyo <etmoyo@gmail.com>
Date: Wed, 16 Apr 2025 13:46:21 -0400
Subject: [PATCH 4/4] updates docs

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index cad16e8..c143d7d 100644
--- a/README.md
+++ b/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`