diff --git a/workflow/qhtcp-workflow b/workflow/qhtcp-workflow
index e5239d09..cdd0aa18 100755
--- a/workflow/qhtcp-workflow
+++ b/workflow/qhtcp-workflow
@@ -86,13 +86,13 @@ print_help() {
 		OPTIONS:
 		  --project, -p PROJECT
 		    PROJECT should follow the pattern ${PROJECT_PREFIX}_PROJECT_NAME
-		  --module, -i MODULE
+		  --module, -i MODULE[,MODULE...]
 		    See MODULES section below for list of available modules
 		    If no --include is specified, all modules are run
 		  --submodule, -s SUBMODULE "[ARG1],[ARG2]..." (string of comma delimited arguments)
 		    See SUBMODULES section below for list of available modules
 		    See documentation for submodule argument usage
-		  --nomodule, -n MODULE
+		  --nomodule, -n MODULE[,MODULE...]
 		    See MODULES and SUBMODULES section below for list of modules to exclude
 		  --markdown
 		    Generate the shdoc markdown README.md file for this program
@@ -332,8 +332,8 @@ print_header() {
   # Let user choose project(s)
   if [[ -z ${PROJECTS[*]} ]]; then
     num=$((${#projects[@]}))
-    echo "Enter project #'s to run (comma delimited)"
-    read -r -p "Or hit enter to add a new project" response
+    echo "Enter comma delimited project #'s (from list) to analyze"
+    read -r -p "Or hit Enter to add a new project" response
     [[ -z $response ]] && ask_pn && PROJECTS+=("${ADD_PROJECTS[@]}")
     ((YES)) || read -r -p "Hit enter for default ($num): " response
     [[ -z $response ]] && response=$num
@@ -346,7 +346,7 @@ print_header() {
 
   if [[ -z ${MODULES[*]} && -z ${INCLUDE_MODULES[*]} && -z ${EXCLUDE_MODULES[*]} ]]; then
     echo "Enter module #'s to run (by #, comma delimited)"
-    ((YES)) || read -r -p "Hit enter for default (ALL): " response
+    ((YES)) || read -r -p "Or hit Enter for default (ALL): " response
     if [[ -n $response ]]; then
       IFS=',' read -ra arr <<< "$response"
       for i in "${arr[@]}"; do
@@ -360,11 +360,10 @@ print_header() {
     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...\""
-      read -r -p "Or hit Enter to continue: " response
+      ((YES)) || read -r -p "Or hit Enter to continue: " response
       [[ -z $response ]] && break
       IFS=' ' read -ra arr <<< "$response"
       if [[ ! ${#arr[@]} -eq 2 ]]; then
-        err "Enter a submodule name followed by its arguments as a case delimited string in quotes" 
         err "The second argument is required and may be an empty string, \"\""
       else
         SUBMODULES+=("${arr[@]}")
@@ -1727,6 +1726,9 @@ main() {
       STUDY_TEMPLATE_DIR STUDY_INFO_FILE
     fi
 
+    debug "Active modules: ${MODULES[*]}"
+    debug "Active submodules and their args: ${SUBMODULES[*]}"
+
     # Run selected modules
     for m in "${MODULES[@]}"; do
       ask "Run $m module?" && "$m"