diff --git a/scripts/func_defs.py b/scripts/func_defs.py
index 7ea7895..4f1f271 100755
--- a/scripts/func_defs.py
+++ b/scripts/func_defs.py
@@ -86,6 +86,12 @@ def bail(msg):
     print(msg, file=sys.stderr)
     exit(1)
 
+
+# print a warning
+def warn(msg):
+    """Print the warning message to stderr."""
+    print(f"WARNING: {msg}", file=sys.stderr)
+
 def TrueOrFalse(value):
     value = repr(value)
     if value:
diff --git a/scripts/validate_config.py b/scripts/validate_config.py
index 58ff969..e9e815c 100644
--- a/scripts/validate_config.py
+++ b/scripts/validate_config.py
@@ -20,7 +20,7 @@
 import os
 import csv
 from glob import glob
-from func_defs import bail
+from func_defs import bail, warn
 
 # ==============================================================================
 #
@@ -101,12 +101,35 @@ def parse_samples(lines):
         outputdict[row[2]] = sampleid_dict
     return { 'SAMPLES': outputdict }
 
+def update_config_layout(config):
+    # check for new annotation layout
+    if not 'differential-methylation' in config['general']:
+        return config
+
+    differential_methylation = config['general']['differential-methylation']
+    if not 'annotation' in differential_methylation:
+        return config
+
+    warn("The specification of annotation files has changed in version 0.1.9 \n"+
+        "For now updating configuration file with the new default settings layout.\n"+
+        "In the future, please retrieve the new default settings layout with 'pigx-bsseq --init settings'.")
+    ## move cpgisland and refgene files to location dict
+    if 'cpgIsland-bedfile' in differential_methylation['annotation']:
+        config['locations']['cpgIsland-bedfile'] = differential_methylation['annotation']['cpgIsland-bedfile']
+    if 'refGenes-bedfile' in differential_methylation['annotation']:
+        config['locations']['refGenes-bedfile'] = differential_methylation['annotation']['refGenes-bedfile']
+    ## remove annotation section
+    differential_methylation.pop('annotation')
+
+    config['general']['differential-methylation'] = differential_methylation
+
+    return config
+
+
 
 # --------------------------------------
 # validation of Config 
 # --------------------------------------
-
-
 # check for common input/configuration errors:
 def validate_config(config):
     # Check that all locations exist
@@ -149,14 +172,6 @@ def validate_config(config):
         bail("ERROR: The specification of treatment groups and differential analysis has changed.\n"+
         "Please retrieve the new default settings layout with 'pigx-bsseq --init settings'.\n")
 
-
-    # check for new annotation layout
-    if 'annotation' in config['general']['differential-methylation']:
-        bail("ERROR: The specification of annotation files has changed.\n"+
-        "Please retrieve the new default settings layout with 'pigx-bsseq --init settings'.\n")
-
-
-
     # Check for a any Assembly string
     if not config['general']['assembly']:
             bail("ERROR: Please set a genome assembly string in the settings file at general::assembly.")
diff --git a/snakefile.py b/snakefile.py
index 257d41c..3cd1045 100644
--- a/snakefile.py
+++ b/snakefile.py
@@ -25,6 +25,7 @@
 include   : os.path.join(config['locations']['pkglibexecdir'], 'scripts/update_pigx_work.py')
 include   : os.path.join(config['locations']['pkglibexecdir'], 'scripts/validate_config.py')
 
+config = update_config_layout(config)
 validate_config(config)
 update_pigx_work(config)