Merge pull request #85 from FredHutch/47-module-usage

Adding module check to HelloModuleHostname

helloModuleHostname/helloModuleHostname.wdl

@@ -1,40 +1,73 @@
 version 1.0
 ## This is a test workflow that returns the hostname of the node 
 ## the job is submitted to as a test for module functionality on Gizmo.
+## Added verification of module loading.
 
 #### WORKFLOW DEFINITION
 
 workflow HelloModuleHostname {
+  input {
+    String module2load = "Python/3.12.3-GCCcore-13.3.0" # Default value can be overwritten
+  }
+
   call Hostname {
+    input:
+      module_env = module2load
   }
 
   output {
     File stdout = Hostname.out
+    Boolean module_loaded = Hostname.module_verified
   }
 
   parameter_meta {
     stdout: "hostname of the node the job was submitted to"
+    module_loaded: "boolean indicating if the specified module was successfully loaded"
   }
 }
 
 #### TASK DEFINITIONS
 
 task Hostname {
+  input {
+    String module_env
+  }
+
   command <<<
-    echo $(hostname)
+    set -e  # Exit on any error
+
+    # Get hostname
+    hostname
+
+    # List loaded modules and verify our module is loaded
+    source /app/lmod/lmod/init/profile
+    module list 2>&1 | tee module_list.txt
+
+    # Check if the module or its base name is in the loaded modules
+    if grep -q "~{module_env}" module_list.txt; then
+      echo "true" > module_verified.txt
+      echo "Successfully verified module ~{module_env} is loaded"
+    else
+      echo "ERROR: Module ~{module_env} was not found in loaded modules:"
+      cat module_list.txt
+      exit 1
+    fi
   >>>
 
   output {
     File out = stdout()
+    Boolean module_verified = read_boolean("module_verified.txt")
   }
 
   runtime {
     cpu: 1
     memory: "1 GB"
-    modules: "Python/3.7.4-foss-2019b-fh1"
+    modules: "~{module_env}"
   }
 
   parameter_meta {
-    out: "hostname of the node the job was submitted to"
+    module_env: "name of modules to be loaded"
+    out: "output file containing hostname and module information"
+    module_verified: "boolean indicating if the requested module was successfully loaded"
   }
 }

helloModuleHostname/inputs.json

@@ -0,0 +1,3 @@
+{
+    "HelloModuleHostname.module2load": "Python/3.12.3-GCCcore-13.3.0"
+}