Beginning debug/cleanup

workflow/qhtcp-workflow

@@ -229,14 +229,19 @@ err() { echo "Error: $*" >&2; }
 ask_pn() {
   unset PROJECT
   declare -g PROJECT
+  example_pn="${PROJECT_PREFIX}_$(random_words 3)"
   cat <<-EOF
-		Enter a new or existing project name, ex. ${PROJECT_PREFIX}_$(random_words 3)
+		Enter a new or existing project name
 		If entering a new project, use the suggested prefix: ${PROJECT_PREFIX}_
 		You may choose any combination of words/characters following the prefix, but be sensible.
 		Make it descriptive and avoid spaces and special characters.
+		Example: ${example_pn}
 	EOF
-  read -r -p "Enter a new or existing project name: " PROJECT
-  [[ -z $PROJECT ]]
+  read -r -p "Enter a new or existing project name ($example_pn): " PROJECT
+  if [[ -z $PROJECT ]]; then
+    echo "Setting project name to the default: $example_pn"
+    PROJECT="$example_pn"
+  fi
 }
 debug() { (( DEBUG )) && echo "Debug: $*"; }
 # Not super portable but nice to have
@@ -691,7 +696,6 @@ qhtcp() {
   STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt"
   QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT"
   APPS_DIR="$QHTCP_PROJECT_DIR/apps"
-  CODE_DIR="$QHTCP_PROJECT_DIR/Code" # legacy location, keeping until can port each script to APPS
   STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
   
   if [[ -d $QHTCP_PROJECT_DIR ]]; then
@@ -1089,7 +1093,7 @@ r_gta_heatmaps() {
 
 	EOF
 
-  script="$CODE_DIR/TSHeatmaps5dev2.R"
+  script="$APPS_DIR/r/TSHeatmaps5dev2.R"
 
   [[ -d $5 ]] || mkdir -p "$5"
 
@@ -1468,9 +1472,9 @@ main() {
       SCANS_DIR="$d"
     fi
   done
-  echo "Scans directory: $SCANS_DIR"
+  echo "Using scans directory: $SCANS_DIR"
   echo "Change the SCANS environment variable to override"
-  echo "Example: SCANS=/path/to/other/scans ./qhtcp-workflow.sh"
+  echo "Example: SCANS=/path/to/scans ./qhtcp-workflow"
 
   # Set the automatic project directory prefix
   PROJECT_USER="$(whoami)"