diff --git a/mess/workflow/Snakefile b/mess/workflow/Snakefile
index 8e89441..d38afb6 100644
--- a/mess/workflow/Snakefile
+++ b/mess/workflow/Snakefile
@@ -131,6 +131,7 @@ else:
 
 
 # reads post-processsing options
+random.seed(SEED)
 SHUFFLE = dict(zip(SAMPLES, random.sample(range(1, 100000), len(SAMPLES))))
 SKIP_SHUFFLE = config.args.skip_shuffle
 RANKS = config.args.ranks
diff --git a/mess/workflow/simulate.smk b/mess/workflow/simulate.smk
index 4f2b23f..580e945 100644
--- a/mess/workflow/simulate.smk
+++ b/mess/workflow/simulate.smk
@@ -110,6 +110,7 @@ else:
 
 
 # reads post-processsing options
+random.seed(SEED)
 SHUFFLE = dict(zip(SAMPLES, random.sample(range(1, 100000), len(SAMPLES))))
 SKIP_SHUFFLE = config.args.skip_shuffle
 RANKS = config.args.ranks