From de370b9a7ee9ed19b997a0dc39b0c9ea6403061f Mon Sep 17 00:00:00 2001
From: tefirman <tefirman@gmail.com>
Date: Tue, 17 Dec 2024 17:05:50 -0800
Subject: [PATCH 1/2] Adding inputs and options jsons to the hello world unit
 tests

---
 helloDockerHostname/inputs.json  | 1 +
 helloDockerHostname/options.json | 5 +++++
 helloHostname/inputs.json        | 1 +
 helloHostname/options.json       | 5 +++++
 helloModuleHostname/inputs.json  | 1 +
 helloModuleHostname/options.json | 5 +++++
 6 files changed, 18 insertions(+)
 create mode 100644 helloDockerHostname/inputs.json
 create mode 100644 helloDockerHostname/options.json
 create mode 100644 helloHostname/inputs.json
 create mode 100644 helloHostname/options.json
 create mode 100644 helloModuleHostname/inputs.json
 create mode 100644 helloModuleHostname/options.json

diff --git a/helloDockerHostname/inputs.json b/helloDockerHostname/inputs.json
new file mode 100644
index 0000000..9e26dfe
--- /dev/null
+++ b/helloDockerHostname/inputs.json
@@ -0,0 +1 @@
+{}
\ No newline at end of file
diff --git a/helloDockerHostname/options.json b/helloDockerHostname/options.json
new file mode 100644
index 0000000..1d043b8
--- /dev/null
+++ b/helloDockerHostname/options.json
@@ -0,0 +1,5 @@
+{
+    "workflow_failure_mode": "ContinueWhilePossible",
+    "write_to_cache": false,
+    "read_from_cache": false
+}
diff --git a/helloHostname/inputs.json b/helloHostname/inputs.json
new file mode 100644
index 0000000..9e26dfe
--- /dev/null
+++ b/helloHostname/inputs.json
@@ -0,0 +1 @@
+{}
\ No newline at end of file
diff --git a/helloHostname/options.json b/helloHostname/options.json
new file mode 100644
index 0000000..1d043b8
--- /dev/null
+++ b/helloHostname/options.json
@@ -0,0 +1,5 @@
+{
+    "workflow_failure_mode": "ContinueWhilePossible",
+    "write_to_cache": false,
+    "read_from_cache": false
+}
diff --git a/helloModuleHostname/inputs.json b/helloModuleHostname/inputs.json
new file mode 100644
index 0000000..9e26dfe
--- /dev/null
+++ b/helloModuleHostname/inputs.json
@@ -0,0 +1 @@
+{}
\ No newline at end of file
diff --git a/helloModuleHostname/options.json b/helloModuleHostname/options.json
new file mode 100644
index 0000000..1d043b8
--- /dev/null
+++ b/helloModuleHostname/options.json
@@ -0,0 +1,5 @@
+{
+    "workflow_failure_mode": "ContinueWhilePossible",
+    "write_to_cache": false,
+    "read_from_cache": false
+}

From a3b8bd14baa6d44e82128a600d042442cd2a2abf Mon Sep 17 00:00:00 2001
From: tefirman <tefirman@gmail.com>
Date: Tue, 17 Dec 2024 17:07:36 -0800
Subject: [PATCH 2/2] Updating matrix approach in yml files to include inputs
 and options jsons

---
 .github/workflows/cromwell-test-run.yml | 8 ++++----
 .github/workflows/womtools-validate.yml | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/cromwell-test-run.yml b/.github/workflows/cromwell-test-run.yml
index 4143d5b..4563f2d 100644
--- a/.github/workflows/cromwell-test-run.yml
+++ b/.github/workflows/cromwell-test-run.yml
@@ -12,9 +12,9 @@ jobs:
     strategy:
       matrix:
         wdl:
-          - helloHostname/helloHostname.wdl
-          - helloModuleHostname/helloModuleHostname.wdl
-          - helloDockerHostname/helloDockerHostname.wdl
+          - helloHostname
+          - helloModuleHostname
+          - helloDockerHostname
     steps:
       -
         name: Checkout
@@ -30,5 +30,5 @@ jobs:
         run: wget -q https://github.com/broadinstitute/cromwell/releases/download/86/cromwell-86.jar
       -
         name: Execute Test Run of WDL Workflows
-        run: java -jar cromwell-86.jar run ${{ matrix.wdl }}
+        run: java -jar cromwell-86.jar run ${{ matrix.wdl }}/${{ matrix.wdl }}.wdl -i ${{ matrix.wdl }}/inputs.json -o ${{ matrix.wdl }}/options.json
 
diff --git a/.github/workflows/womtools-validate.yml b/.github/workflows/womtools-validate.yml
index afe5bdc..09276fa 100644
--- a/.github/workflows/womtools-validate.yml
+++ b/.github/workflows/womtools-validate.yml
@@ -15,9 +15,9 @@ jobs:
     strategy:
       matrix:
         wdl:
-          - helloHostname/helloHostname.wdl
-          - helloModuleHostname/helloModuleHostname.wdl
-          - helloDockerHostname/helloDockerHostname.wdl
+          - helloHostname
+          - helloModuleHostname
+          - helloDockerHostname
     steps:
       -
         name: Checkout
@@ -33,7 +33,7 @@ jobs:
         run: wget -q https://github.com/broadinstitute/cromwell/releases/download/86/womtool-86.jar
       -
         name: Validate WDL Scripts
-        run: java -jar womtool-86.jar validate ${{ matrix.wdl }}
+        run: java -jar womtool-86.jar validate ${{ matrix.wdl }}/${{ matrix.wdl }}.wdl -i ${{ matrix.wdl }}/inputs.json