From fe2a7831694701b5b326f02721c8e695a2904e91 Mon Sep 17 00:00:00 2001
From: cellgeni <cellgeni@sanger.ac.uk>
Date: Mon, 20 Jan 2025 16:32:21 +0000
Subject: [PATCH] Added full paths

---
 tests/test_metadata.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_metadata.sh b/tests/test_metadata.sh
index 491e74d..bed7a39 100644
--- a/tests/test_metadata.sh
+++ b/tests/test_metadata.sh
@@ -8,7 +8,7 @@ fi
 
 SERIES=$1
 SAMPLE_LIST=${2:-""}
-OUTPUT_DIR="output/$SERIES"
+OUTPUT_DIR="${GITHUB_WORKSPACE}/output/$SERIES"
 
 # Create output directory and copy all scripts
 mkdir -p $OUTPUT_DIR
@@ -20,7 +20,7 @@ echo "Loading metadata for $SERIES $SAMPLE_LIST"
 ./collect_metadata.sh $SERIES $SAMPLE_LIST
 
 # Test output
-for file in test_data/$SERIES/*
+for file in ${GITHUB_WORKSPACE}/test_data/$SERIES/*
 do
   filename=$(basename $file)
   echo "Testing $file"
@@ -40,7 +40,7 @@ do
   fi
 
   # Compare the actual output with the expected output
-  if ! diff -q $filename $file
+  if [[ ! diff -q $filename $file ]]
   then
     echo "❌ERROR: Output file $filename does not match expected output!"
     exit 1