diff --git a/workflow/qhtcp-workflow b/workflow/qhtcp-workflow
index 89441ffe..409fd319 100755
--- a/workflow/qhtcp-workflow
+++ b/workflow/qhtcp-workflow
@@ -130,7 +130,8 @@ print_help() {
 
 # @section User Input
 # @set PROJECTS array List of projects to work on
-# @set INCLUDE_MODULES array List of modules to run
+# @set MODULES array List of modules to run
+# @set SUBMODULES array List of submodules and their arguments to run
 # @set EXCLUDE_MODULES array List of modules not to run
 # @set DEBUG int Turn debugging on
 # @set YES int Turn assume yes on
@@ -152,7 +153,7 @@ parse_input() {
             ;;
         --module|-m)
             shift
-            IFS=',' read -ra INCLUDE_MODULES <<< "$1"
+            IFS=',' read -ra MODULES <<< "$1"
             ;;
         --submodule|-s)
             shift
@@ -344,7 +345,7 @@ print_header() {
     unset response arr i
   fi
 
-  if [[ -z ${MODULES[*]} && -z ${INCLUDE_MODULES[*]} && -z ${EXCLUDE_MODULES[*]} ]]; then
+  if [[ -z ${MODULES[*]} && -z ${EXCLUDE_MODULES[*]} ]]; then
     echo "Enter module #'s to run (by #, comma delimited)"
     ((YES)) || read -r -p "Or hit Enter for default (ALL): " response
     if [[ -n $response ]]; then
@@ -356,7 +357,7 @@ print_header() {
     unset response arr i
   fi
 
-  if [[ -z ${MODULES[*]} && -z ${INCLUDE_MODULES[*]} && -z ${EXCLUDE_MODULES[*]} && -z ${SUBMODULES[*]} ]]; then
+  if [[ -z ${MODULES[*]} && -z ${EXCLUDE_MODULES[*]} && -z ${SUBMODULES[*]} ]]; then
     while :; do
       echo "Enter a submodule followed by its arguments as a case delimited string in quotes"
       echo "Example: ${ALL_SUBMODULES[0]} \"arg1,arg2,arg3...\""
@@ -1668,20 +1669,10 @@ main() {
     fi
   done
 
-  # If we don't catch with getopt or env, run all
-  if [[ ${#INCLUDE_MODULES[@]} -eq 0 ]]; then
-    MODULES=("${ALL_MODULES[@]}")
-  else
-    MODULES=("${INCLUDE_MODULES[@]}")
-  fi
-
   # Exclude modules from --exclude
-  arr=()
-  for m in "${MODULES[@]}"; do
-    [[ " ${EXCLUDE_MODULES[*]} " =~ [[:space:]]${m}[[:space:]] ]] || arr+=("$m")
+  for i in "${!MODULES[@]}"; do
+    [[ " ${EXCLUDE_MODULES[*]} " =~ [[:space:]]${MODULES[i]}[[:space:]] ]] && unset "MODULES[i]"
   done
-  MODULES=("${arr[@]}")
-  unset arr
     
   # Sanitize MODULES
   for i in "${!MODULES[@]}"; do