From e302c09128e91a39acb19958a69d5a45847bb57d Mon Sep 17 00:00:00 2001
From: aofarrel <aofarrel@ucsc.edu>
Date: Fri, 23 Sep 2022 13:26:17 -0700
Subject: [PATCH 1/7] simple example of scattering on a struct

---
 wholet.wdl | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 wholet.wdl

diff --git a/wholet.wdl b/wholet.wdl
new file mode 100644
index 0000000..7fde569
--- /dev/null
+++ b/wholet.wdl
@@ -0,0 +1,30 @@
+version 1.0
+
+struct Dog {
+	String breed
+	Float age_years
+}
+
+task out {
+	input {
+		Dog who
+	}
+    command <<<
+        echo "I can see a ~{who.breed} that is ~{who.age_years} years old"
+    >>>
+}
+
+workflow wholet {
+
+	Dog pompey = {"breed": "King Charles Cavalier Spaniel", "age_years": 4.5}
+	Dog gremlin = {"breed": "kind of weird terrier", "age_years": 0.3}
+
+	Array[Dog] thedogs = [pompey, gremlin]
+
+    scatter(dog in thedogs) {
+    	call out {
+	        input:
+	            who = dog
+	    }
+	}
+}
\ No newline at end of file

From c2f4d46a06b11e6cface3ddd62b1534532f18f5b Mon Sep 17 00:00:00 2001
From: aofarrel <aofarrel@ucsc.edu>
Date: Fri, 23 Sep 2022 13:41:02 -0700
Subject: [PATCH 2/7] Add a scattered array

---
 data/permit.md |  3 +++
 wholet.json    |  4 ++++
 wholet.wdl     | 15 +++++++++++++--
 3 files changed, 20 insertions(+), 2 deletions(-)
 create mode 100644 data/permit.md
 create mode 100644 wholet.json

diff --git a/data/permit.md b/data/permit.md
new file mode 100644
index 0000000..b267014
--- /dev/null
+++ b/data/permit.md
@@ -0,0 +1,3 @@
+# Official Permit
+
+I can do what I want.
\ No newline at end of file
diff --git a/wholet.json b/wholet.json
new file mode 100644
index 0000000..cfda54f
--- /dev/null
+++ b/wholet.json
@@ -0,0 +1,4 @@
+{
+    "pompey_permit": "data/permit.md",
+    "gremlin_permit": "data/permit.md"
+}
\ No newline at end of file
diff --git a/wholet.wdl b/wholet.wdl
index 7fde569..4fb8a9f 100644
--- a/wholet.wdl
+++ b/wholet.wdl
@@ -3,6 +3,7 @@ version 1.0
 struct Dog {
 	String breed
 	Float age_years
+	File permit
 }
 
 task out {
@@ -11,13 +12,23 @@ task out {
 	}
     command <<<
         echo "I can see a ~{who.breed} that is ~{who.age_years} years old"
+        cat ~{who.permit}
     >>>
+
+    runtime {
+		docker: "ubuntu:latest"
+		preemptible: 1
+	}
 }
 
 workflow wholet {
+	input {
+		File pompey_permit
+		File gremlin_permit
+	}
 
-	Dog pompey = {"breed": "King Charles Cavalier Spaniel", "age_years": 4.5}
-	Dog gremlin = {"breed": "kind of weird terrier", "age_years": 0.3}
+	Dog pompey = {"breed": "King Charles Cavalier Spaniel", "age_years": 4.5, "permit": pompey_permit}
+	Dog gremlin = {"breed": "kind of weird terrier", "age_years": 0.3, "permit": gremlin_permit}
 
 	Array[Dog] thedogs = [pompey, gremlin]
 

From 1597ad7aed54f53619443a7c887cf07e61ce8a8f Mon Sep 17 00:00:00 2001
From: aofarrel <aofarrel@ucsc.edu>
Date: Fri, 23 Sep 2022 14:07:58 -0700
Subject: [PATCH 3/7] Input as array (passes on terra)

---
 wholet.json | 3 +--
 wholet.wdl  | 7 +++----
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/wholet.json b/wholet.json
index cfda54f..e7dbf3a 100644
--- a/wholet.json
+++ b/wholet.json
@@ -1,4 +1,3 @@
 {
-    "pompey_permit": "data/permit.md",
-    "gremlin_permit": "data/permit.md"
+    "files": ["data/permit.md", "data/permit.md"]
 }
\ No newline at end of file
diff --git a/wholet.wdl b/wholet.wdl
index 4fb8a9f..957756b 100644
--- a/wholet.wdl
+++ b/wholet.wdl
@@ -23,12 +23,11 @@ task out {
 
 workflow wholet {
 	input {
-		File pompey_permit
-		File gremlin_permit
+		Array[File] files
 	}
 
-	Dog pompey = {"breed": "King Charles Cavalier Spaniel", "age_years": 4.5, "permit": pompey_permit}
-	Dog gremlin = {"breed": "kind of weird terrier", "age_years": 0.3, "permit": gremlin_permit}
+	Dog pompey = {"breed": "King Charles Cavalier Spaniel", "age_years": 4.5, "permit": files[0]}
+	Dog gremlin = {"breed": "kind of weird terrier", "age_years": 0.3, "permit": files[1]}
 
 	Array[Dog] thedogs = [pompey, gremlin]
 

From 0d65c80ce3b1100ebe417eb85ddd058b9a255c32 Mon Sep 17 00:00:00 2001
From: aofarrel <aofarrel@ucsc.edu>
Date: Fri, 23 Sep 2022 14:13:22 -0700
Subject: [PATCH 4/7] nested array test (fails)

---
 wholet.json | 2 +-
 wholet.wdl  | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/wholet.json b/wholet.json
index e7dbf3a..24301e3 100644
--- a/wholet.json
+++ b/wholet.json
@@ -1,3 +1,3 @@
 {
-    "files": ["data/permit.md", "data/permit.md"]
+    "wholet.files": [["data/permit.md", "data/permit.md"],["data/permit.md", "data/permit.md"]]
 }
\ No newline at end of file
diff --git a/wholet.wdl b/wholet.wdl
index 957756b..24d8754 100644
--- a/wholet.wdl
+++ b/wholet.wdl
@@ -3,7 +3,7 @@ version 1.0
 struct Dog {
 	String breed
 	Float age_years
-	File permit
+	Array[File] permit
 }
 
 task out {
@@ -12,7 +12,7 @@ task out {
 	}
     command <<<
         echo "I can see a ~{who.breed} that is ~{who.age_years} years old"
-        cat ~{who.permit}
+        cat ~{sep='' who.permit}
     >>>
 
     runtime {
@@ -23,7 +23,7 @@ task out {
 
 workflow wholet {
 	input {
-		Array[File] files
+		Array[Array[File]] files
 	}
 
 	Dog pompey = {"breed": "King Charles Cavalier Spaniel", "age_years": 4.5, "permit": files[0]}

From 0d8f9b920d48f38c309c7350100aa9cf199b4a65 Mon Sep 17 00:00:00 2001
From: aofarrel <aofarrel@ucsc.edu>
Date: Mon, 26 Sep 2022 12:05:37 -0700
Subject: [PATCH 5/7] Create wholet-nested.wdl

---
 wholet-nested.wdl | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 wholet-nested.wdl

diff --git a/wholet-nested.wdl b/wholet-nested.wdl
new file mode 100644
index 0000000..f63aa5d
--- /dev/null
+++ b/wholet-nested.wdl
@@ -0,0 +1,42 @@
+# This is not a valid WDL. I'm not quite sure why. Compare to the functional wholet.wdl
+
+version 1.0
+
+struct Dog {
+	String breed
+	Float age_years
+	Array[File] permit
+}
+
+task out {
+	input {
+		Dog who
+	}
+    command <<<
+        echo "I can see a ~{who.breed} that is ~{who.age_years} years old"
+        cat ~{sep='' who.permit}
+    >>>
+
+    runtime {
+		docker: "ubuntu:latest"
+		preemptible: 1
+	}
+}
+
+workflow wholet {
+	input {
+		Array[Array[File]] files
+	}
+
+	Dog pompey = {"breed": "King Charles Cavalier Spaniel", "age_years": 4.5, "permit": files[0]}
+	Dog gremlin = {"breed": "kind of weird terrier", "age_years": 0.3, "permit": files[1]}
+
+	Array[Dog] thedogs = [pompey, gremlin]
+
+    scatter(dog in thedogs) {
+    	call out {
+	        input:
+	            who = dog
+	    }
+	}
+}
\ No newline at end of file

From 06f84a2e00d5a83d49ecea69b89057910f4d7f0d Mon Sep 17 00:00:00 2001
From: aofarrel <aofarrel@ucsc.edu>
Date: Mon, 26 Sep 2022 12:05:42 -0700
Subject: [PATCH 6/7] Revert "nested array test (fails)"

This reverts commit 0d65c80ce3b1100ebe417eb85ddd058b9a255c32.
---
 wholet.json | 2 +-
 wholet.wdl  | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/wholet.json b/wholet.json
index 24301e3..e7dbf3a 100644
--- a/wholet.json
+++ b/wholet.json
@@ -1,3 +1,3 @@
 {
-    "wholet.files": [["data/permit.md", "data/permit.md"],["data/permit.md", "data/permit.md"]]
+    "files": ["data/permit.md", "data/permit.md"]
 }
\ No newline at end of file
diff --git a/wholet.wdl b/wholet.wdl
index 24d8754..957756b 100644
--- a/wholet.wdl
+++ b/wholet.wdl
@@ -3,7 +3,7 @@ version 1.0
 struct Dog {
 	String breed
 	Float age_years
-	Array[File] permit
+	File permit
 }
 
 task out {
@@ -12,7 +12,7 @@ task out {
 	}
     command <<<
         echo "I can see a ~{who.breed} that is ~{who.age_years} years old"
-        cat ~{sep='' who.permit}
+        cat ~{who.permit}
     >>>
 
     runtime {
@@ -23,7 +23,7 @@ task out {
 
 workflow wholet {
 	input {
-		Array[Array[File]] files
+		Array[File] files
 	}
 
 	Dog pompey = {"breed": "King Charles Cavalier Spaniel", "age_years": 4.5, "permit": files[0]}

From 6b46b4063ae8e2d5d0a38c09bf75b4f5a97bac00 Mon Sep 17 00:00:00 2001
From: aofarrel <aofarrel@ucsc.edu>
Date: Thu, 27 Oct 2022 10:19:21 -0700
Subject: [PATCH 7/7] Clearer testing

---
 wholet-nested.json | 3 +++
 wholet-nested.wdl  | 4 ++++
 wholet.json        | 4 ++--
 wholet.wdl         | 4 ++++
 4 files changed, 13 insertions(+), 2 deletions(-)
 create mode 100644 wholet-nested.json

diff --git a/wholet-nested.json b/wholet-nested.json
new file mode 100644
index 0000000..400005e
--- /dev/null
+++ b/wholet-nested.json
@@ -0,0 +1,3 @@
+{
+  "wholet.files": [["data/permit.md"], ["data/permit.md"]],
+}
diff --git a/wholet-nested.wdl b/wholet-nested.wdl
index f63aa5d..333551d 100644
--- a/wholet-nested.wdl
+++ b/wholet-nested.wdl
@@ -21,6 +21,10 @@ task out {
 		docker: "ubuntu:latest"
 		preemptible: 1
 	}
+
+	output {
+		Dog out = who
+	}
 }
 
 workflow wholet {
diff --git a/wholet.json b/wholet.json
index e7dbf3a..5328414 100644
--- a/wholet.json
+++ b/wholet.json
@@ -1,3 +1,3 @@
 {
-    "files": ["data/permit.md", "data/permit.md"]
-}
\ No newline at end of file
+  "wholet.files": ["data/permit.md", "data/permit.md"],
+}
diff --git a/wholet.wdl b/wholet.wdl
index 957756b..06e613c 100644
--- a/wholet.wdl
+++ b/wholet.wdl
@@ -19,6 +19,10 @@ task out {
 		docker: "ubuntu:latest"
 		preemptible: 1
 	}
+
+	output {
+		Dog out = who
+	}
 }
 
 workflow wholet {