diff --git a/snakemake/utils.py b/snakemake/utils.py
index 3cc81c28b..0d427c3fc 100644
--- a/snakemake/utils.py
+++ b/snakemake/utils.py
@@ -479,7 +479,7 @@ def min_version(version):
 
 
 def update_config(config, overwrite_config):
-    """Recursively update dictionary config with overwrite_config.
+    """Recursively update dictionary config with overwrite_config in-place.
 
     See
     https://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth
@@ -488,18 +488,25 @@ def update_config(config, overwrite_config):
     Args:
       config (dict): dictionary to update
       overwrite_config (dict): dictionary whose items will overwrite those in config
-
     """
 
-    def _update(d, u):
-        for key, value in u.items():
+    def _update_config(config, overwrite_config):
+        """Necessary as recursive calls require a return value,
+        but `update_config()` has no return value.
+        """
+        for key, value in overwrite_config.items():
+            if not isinstance(config, collections.abc.Mapping):
+                # the config cannot be updated as it is no dict
+                # -> just overwrite it with the new value
+                config = {}
             if isinstance(value, collections.abc.Mapping):
-                d[key] = _update(d.get(key, {}), value)
+                sub_config = config.get(key, {})
+                config[key] = _update_config(sub_config, value)
             else:
-                d[key] = value
-        return d
+                config[key] = value
+        return config
 
-    _update(config, overwrite_config)
+    _update_config(config, overwrite_config)
 
 
 def available_cpu_count():
diff --git a/tests/common.py b/tests/common.py
index 8d1a0328a..383aa2930 100644
--- a/tests/common.py
+++ b/tests/common.py
@@ -33,9 +33,9 @@ def dpath(path):
 def md5sum(filename, ignore_newlines=False):
     if ignore_newlines:
         with open(filename, "r", encoding="utf-8", errors="surrogateescape") as f:
-            data = f.read().encode("utf8", errors="surrogateescape")
+            data = f.read().strip().encode("utf8", errors="surrogateescape")
     else:
-        data = open(filename, "rb").read()
+        data = open(filename, "rb").read().strip()
     return hashlib.md5(data).hexdigest()
 
 
@@ -285,9 +285,9 @@ def run(
                 md5target = md5sum(targetfile, ignore_newlines=ON_WINDOWS)
                 if md5target != md5expected:
                     with open(expectedfile) as expected:
-                        expected_content = expected.read()
+                        expected_content = expected.read().strip()
                     with open(targetfile) as target:
-                        content = target.read()
+                        content = target.read().strip()
                     assert (
                         False
                     ), "wrong result produced for file '{resultfile}':\n------found------\n{content}\n-----expected-----\n{expected_content}\n-----------------".format(
diff --git a/tests/test_config_merging/config_cmdline_01.yaml b/tests/test_config_merging/config_cmdline_01.yaml
index fc731e9b5..7f8c8e018 100644
--- a/tests/test_config_merging/config_cmdline_01.yaml
+++ b/tests/test_config_merging/config_cmdline_01.yaml
@@ -2,3 +2,5 @@ block:
     foo: cfg01_foo
     bar: cfg01_bar
     baz: cfg01_baz
+    foobar:
+        cfg01_key: cfg01_val
diff --git a/tests/test_config_merging/config_snakefile.yaml b/tests/test_config_merging/config_snakefile.yaml
index c5fbe0a86..fd951ab16 100644
--- a/tests/test_config_merging/config_snakefile.yaml
+++ b/tests/test_config_merging/config_snakefile.yaml
@@ -1,3 +1,4 @@
 block:
     bar: snake_bar
     fubar: snake_fubar
+    foobar: null
diff --git a/tests/test_config_merging/expected-results/test.out b/tests/test_config_merging/expected-results/test.out
index 967372364..96229e319 100644
--- a/tests/test_config_merging/expected-results/test.out
+++ b/tests/test_config_merging/expected-results/test.out
@@ -1 +1 @@
-{"block": {"bar": "cfg01_bar", "baz": "cfg01_baz", "bowser": "cmdline_bowser", "foo": "cfg02_foo", "fubar": "snake_fubar", "qux": "cfg02_qux", "toad": "cmdline_toad"}}
\ No newline at end of file
+{"block": {"bar": "cfg01_bar", "baz": "cfg01_baz", "bowser": "cmdline_bowser", "foo": "cfg02_foo", "foobar": {"cfg01_key": "cfg01_val"}, "fubar": "snake_fubar", "qux": "cfg02_qux", "toad": "cmdline_toad"}}