_helpers: add inplace keyword argument to update_config_from_wildcards

rules/common.smk

@@ -10,6 +10,7 @@ import os, sys, glob
 path = workflow.source_path("../scripts/_helpers.py")
 sys.path.insert(0, os.path.dirname(path))
 
+from _helpers import validate_checksum, update_config_from_wildcards
 from snakemake.utils import update_config
 
 
@@ -41,7 +42,10 @@ def scenario_config(scenario_name):
 
 def static_getter(wildcards, keys, default):
     """Getter function for static config values."""
-    return get_config(config, keys, default)
+    config_with_wildcards = update_config_from_wildcards(
+        config, wildcards, inplace=False
+    )
+    return get_config(config_with_wildcards, keys, default)
 
 
 def dynamic_getter(wildcards, keys, default):
@@ -53,7 +57,11 @@ def dynamic_getter(wildcards, keys, default):
         raise ValueError(
             f"Scenario {scenario_name} not found in file {config['run']['scenario']['file']}."
         )
-    return get_config(scenario_config(scenario_name), keys, default)
+    config_with_scenario = scenario_config(scenario_name)
+    config_with_wildcards = update_config_from_wildcards(
+        config_with_scenario, wildcards, inplace=False
+    )
+    return get_config(config_with_wildcards, keys, default)
 
 
 def config_provider(*keys, default=None):

scripts/_helpers.py

@@ -8,6 +8,7 @@ import hashlib
 import logging
 import os
 import re
+import copy
 import urllib
 from functools import partial
 from pathlib import Path
@@ -469,13 +470,14 @@ def parse(infix):
         return {infix.pop(0): parse(infix)}
 
 
-def update_config_from_wildcards(config, w):
+def update_config_from_wildcards(config, w, inplace=True):
     """
     Parses configuration settings from wildcards and updates the config.
-
-    - TODO: Should be run inside config_provider function.
     """
 
+    if not inplace:
+        config = copy.deepcopy(config)
+
     if w.get("opts"):
         opts = w.opts.split("-")
 
@@ -641,6 +643,9 @@ def update_config_from_wildcards(config, w):
                 infix = o.split("+")[1:]
                 update_config(config, parse(infix))
 
+    if not inplace:
+        return config
+
 
 def get_checksum_from_zenodo(file_url):
     parts = file_url.split("/")