diff --git a/scripts/_helpers.py b/scripts/_helpers.py
index ceeb69f9..f7f1c557 100644
--- a/scripts/_helpers.py
+++ b/scripts/_helpers.py
@@ -295,7 +295,7 @@ def get_aggregation_strategies(aggregation_strategies):
     return bus_strategies, generator_strategies
 
 
-def mock_snakemake(rulename, **wildcards):
+def mock_snakemake(rulename, configfiles=[], **wildcards):
     """
     This function is expected to be executed from the 'scripts'-directory of '
     the snakemake project. It returns a snakemake.script.Snakemake object,
@@ -307,6 +307,8 @@ def mock_snakemake(rulename, **wildcards):
     ----------
     rulename: str
         name of the rule for which the snakemake object should be generated
+    configfiles: list, str
+        list of configfiles to be used to update the config
     **wildcards:
         keyword arguments fixing the wildcards. Only necessary if wildcards are
         needed.
@@ -319,46 +321,66 @@ def mock_snakemake(rulename, **wildcards):
     from snakemake.script import Snakemake
 
     script_dir = Path(__file__).parent.resolve()
-    assert (
-        Path.cwd().resolve() == script_dir
-    ), f"mock_snakemake has to be run from the repository scripts directory {script_dir}"
-    os.chdir(script_dir.parent)
-    for p in sm.SNAKEFILE_CHOICES:
-        if os.path.exists(p):
-            snakefile = p
-            break
-    kwargs = dict(rerun_triggers=[]) if parse(sm.__version__) > Version("7.7.0") else {}
-    workflow = sm.Workflow(snakefile, overwrite_configfiles=[], **kwargs)
-    workflow.include(snakefile)
-    workflow.global_resources = {}
-    rule = workflow.get_rule(rulename)
-    dag = sm.dag.DAG(workflow, rules=[rule])
-    wc = Dict(wildcards)
-    job = sm.jobs.Job(rule, dag, wc)
+    root_dir = script_dir.parent
 
-    def make_accessable(*ios):
-        for io in ios:
-            for i in range(len(io)):
-                io[i] = os.path.abspath(io[i])
+    user_in_script_dir = Path.cwd().resolve() == script_dir
+    if user_in_script_dir:
+        os.chdir(root_dir)
+    elif Path.cwd().resolve() != root_dir:
+        raise RuntimeError(
+            "mock_snakemake has to be run from the repository root"
+            f" {root_dir} or scripts directory {script_dir}"
+        )
+    try:
+        for p in sm.SNAKEFILE_CHOICES:
+            if os.path.exists(p):
+                snakefile = p
+                break
+        kwargs = (
+            dict(rerun_triggers=[]) if parse(sm.__version__) > Version("7.7.0") else {}
+        )
+        workflow = sm.Workflow(snakefile, **kwargs)
+        workflow.include(snakefile)
 
-    make_accessable(job.input, job.output, job.log)
-    snakemake = Snakemake(
-        job.input,
-        job.output,
-        job.params,
-        job.wildcards,
-        job.threads,
-        job.resources,
-        job.log,
-        job.dag.workflow.config,
-        job.rule.name,
-        None,
-    )
-    # create log and output dir if not existent
-    for path in list(snakemake.log) + list(snakemake.output):
-        Path(path).parent.mkdir(parents=True, exist_ok=True)
+        if isinstance(configfiles, str):
+            configfiles = [configfiles]
+        if configfiles:
+            for f in configfiles:
+                if not os.path.exists(f):
+                    raise FileNotFoundError(f"Config file {f} does not exist.")
+                workflow.configfile(f)
 
-    os.chdir(script_dir)
+        workflow.global_resources = {}
+        rule = workflow.get_rule(rulename)
+        dag = sm.dag.DAG(workflow, rules=[rule])
+        wc = Dict(wildcards)
+        job = sm.jobs.Job(rule, dag, wc)
+
+        def make_accessable(*ios):
+            for io in ios:
+                for i in range(len(io)):
+                    io[i] = os.path.abspath(io[i])
+
+        make_accessable(job.input, job.output, job.log)
+        snakemake = Snakemake(
+            job.input,
+            job.output,
+            job.params,
+            job.wildcards,
+            job.threads,
+            job.resources,
+            job.log,
+            job.dag.workflow.config,
+            job.rule.name,
+            None,
+        )
+        # create log and output dir if not existent
+        for path in list(snakemake.log) + list(snakemake.output):
+            Path(path).parent.mkdir(parents=True, exist_ok=True)
+
+    finally:
+        if user_in_script_dir:
+            os.chdir(script_dir)
     return snakemake