From 124c7696ba75eba24e00f9203d87eb560e8c8128 Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Wed, 31 Jul 2024 15:29:42 -0400
Subject: [PATCH] Fix out_dir

---
 workflow/qhtcp-workflow | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/workflow/qhtcp-workflow b/workflow/qhtcp-workflow
index 8c4eb123..ad7556c6 100755
--- a/workflow/qhtcp-workflow
+++ b/workflow/qhtcp-workflow
@@ -1479,18 +1479,11 @@ documentation() {
 main() {
   debug "Running: ${FUNCNAME[0]}" "$@"
   
-  # Where are we located?
+  # Where are we
   SCRIPT=$(realpath -s "${BASH_SOURCE[0]}")
   SCRIPT_DIR=$(dirname "$SCRIPT")
 
   # Global directory variables
-  local out_heirarchy=("$OUT_DIR" "$SCRIPT_DIR/out" "/mnt/data/out")
-  for d in "${out_heirarchy[@]}"; do
-    if [[ -d $d ]]; then
-      debug "Using output directory: $d"
-      OUT_DIR="$d"
-    fi
-  done
   TEMPLATES_DIR="$SCRIPT_DIR/templates"
   APPS_DIR="$SCRIPT_DIR/apps"
   DATE="$(date +%Y%m%d)" # change in EASYConsole.m to match
@@ -1515,6 +1508,14 @@ main() {
   echo "Change the SCANS environment variable to override"
   echo "Example: SCANS=/path/to/scans ./qhtcp-workflow"
 
+  local out_heirarchy=("$(dirname "$SCANS_DIR")/out" "$SCRIPT_DIR/out" "/mnt/data/out")
+  for d in "${out_heirarchy[@]}"; do
+    if [[ -d $d ]]; then
+      debug "Using output directory: $d"
+      OUT_DIR="$d"
+    fi
+  done
+
   # Set the automatic project directory prefix
   PROJECT_USER="$(whoami)"
   PROJECT_PREFIX="${DATE}_${PROJECT_USER}" # reversed these so easier to sort and parse date