From d0a7bf243c5df204136fa1f14706aab793793c68 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20K=C3=B6ster?= <johannes.koester@uni-due.de>
Date: Wed, 17 Nov 2021 15:05:26 +0100
Subject: [PATCH] fix: handle config file extension/overwriting more explicitly
 (#1251)

* handle config file extension/overwriting more explicitly

* fmt
---
 snakemake/__init__.py |  4 +++-
 snakemake/workflow.py | 21 +++++++++++++++++----
 2 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/snakemake/__init__.py b/snakemake/__init__.py
index 917ea12ae..88838c080 100644
--- a/snakemake/__init__.py
+++ b/snakemake/__init__.py
@@ -1239,7 +1239,9 @@ def get_argument_parser(profile=None):
             "Specify or overwrite the config file of the workflow (see the docs). "
             "Values specified in JSON or YAML format are available in the global config "
             "dictionary inside the workflow. Multiple files overwrite each other in "
-            "the given order."
+            "the given order. Thereby missing keys in previous config files are extended by "
+            "following configfiles. Note that this order also includes a config file defined "
+            "in the workflow definition itself (which will come first)."
         ),
     )
     group_exec.add_argument(
diff --git a/snakemake/workflow.py b/snakemake/workflow.py
index 93121023d..fb4a23159 100644
--- a/snakemake/workflow.py
+++ b/snakemake/workflow.py
@@ -1238,10 +1238,23 @@ def configfile(self, fp):
         """Update the global config with data from the given file."""
         global config
         if not self.modifier.skip_configfile:
-            self.configfiles.append(fp)
-            c = snakemake.io.load_configfile(fp)
-            update_config(config, c)
-            update_config(config, self.overwrite_config)
+            if os.path.exists(fp):
+                self.configfiles.append(fp)
+                c = snakemake.io.load_configfile(fp)
+                update_config(config, c)
+                if self.overwrite_config:
+                    logger.info(
+                        "Config file {} is extended by additional config specified via the command line.".format(
+                            fp
+                        )
+                    )
+                    update_config(config, self.overwrite_config)
+            elif not self.overwrite_configfiles:
+                raise WorkflowError(
+                    "Workflow defines configfile {} but it is not present or accessible.".format(
+                        fp
+                    )
+                )
 
     def pepfile(self, path):
         global pep