diff --git a/Snakefile b/Snakefile
index fed3c3c0a2364d3cd10f1c29b05b28de9c6f4d34..e9e5244f2f6ca3651a4fae889d13802721dcd91e 100644
--- a/Snakefile
+++ b/Snakefile
@@ -55,7 +55,10 @@ MEMTOTAL = os.environ.get("MEMTOTAL", config['memory_total_gb'])
 MEMCORE = os.environ.get("MEMCORE", config['memory_per_core_gb'])
 
 # temporary directory will be stored inside the OUTPUTDIR directory
+# unless a absolute path is set
 TMPDIR = os.environ.get("TMPDIR", config['tmp_dir'])
+if not os.path.isabs(TMP_DIR):
+    TMPDIR = os.path.join(OUTPUTDIR, TMP_DIR)
 
 
 def prepare_environment(stepname):