From 5fc39f89d8e2701c078337602a899f348b4f6e0a Mon Sep 17 00:00:00 2001
From: stxue1 <stxue@ucsc.edu>
Date: Mon, 30 Sep 2024 13:26:49 -0700
Subject: [PATCH 1/4] Delete conflicting exclude_output section, fix wrong var,
 missing outputs

---
 SPEC.md | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/SPEC.md b/SPEC.md
index 7dc9a32a..79b41f8b 100644
--- a/SPEC.md
+++ b/SPEC.md
@@ -1312,7 +1312,7 @@ workflow string_to_file {
   File path2 = path1
 
   output {
-    Boolean paths_equal = infile == path3
+    Boolean paths_equal = infile == path2
   }
 }
 ```
@@ -3943,14 +3943,6 @@ Example output:
   "optional_output.file_array": ["example1.txt", null]
 }
 ```
-
-Test config:
-
-```json
-{
-  "exclude_output": ["example1", "file_array"]
-}
-```
 </p>
 </details>
 
@@ -8594,6 +8586,8 @@ Example output:
 
 ```json
 {
+  "test_transpose.expected": [[0, 3], [1, 4], [2, 5]],
+  "test_transpose.out": [[0, 3], [1, 4], [2, 5]],
   "test_transpose.is_true": true
 }
 ```

From 5c4845057c057a8d6b22d9c1804e1cdab7c8a010 Mon Sep 17 00:00:00 2001
From: stxue1 <stxue@ucsc.edu>
Date: Mon, 30 Sep 2024 14:56:37 -0700
Subject: [PATCH 2/4] Fix wc command

---
 SPEC.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/SPEC.md b/SPEC.md
index 79b41f8b..8c7c6df7 100644
--- a/SPEC.md
+++ b/SPEC.md
@@ -4573,7 +4573,7 @@ task test_hints {
   }
 
   command <<<
-  wc -l ~{foo}
+  wc -l < ~{foo}
   >>>
 
   output {

From 89c5195ebe5f7fa9ce8b83eec97b0746869f6358 Mon Sep 17 00:00:00 2001
From: stxue1 <stxue@ucsc.edu>
Date: Mon, 30 Sep 2024 15:13:11 -0700
Subject: [PATCH 3/4] Change incorrect json output

---
 SPEC.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/SPEC.md b/SPEC.md
index 8c7c6df7..185a632e 100644
--- a/SPEC.md
+++ b/SPEC.md
@@ -4608,7 +4608,7 @@ Example output:
 
 ```json
 {
-  "test_hints.num_lines": 3
+  "test_hints.num_lines": 2
 }
 ```
 </p>

From 99023782e7f5c2111e130fcafb0200c375b7e7b0 Mon Sep 17 00:00:00 2001
From: stxue1 <stxue@ucsc.edu>
Date: Mon, 30 Sep 2024 15:23:12 -0700
Subject: [PATCH 4/4] Add missing output

---
 SPEC.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/SPEC.md b/SPEC.md
index 185a632e..13e47531 100644
--- a/SPEC.md
+++ b/SPEC.md
@@ -4693,7 +4693,9 @@ Example input:
 Example output:
 
 ```json
-{}
+{
+  "input_hint.experience": []
+}
 ```
 </p>
 </details>