diff --git a/looper/cli_pydantic.py b/looper/cli_pydantic.py
index 669c7f65..16bb6206 100644
--- a/looper/cli_pydantic.py
+++ b/looper/cli_pydantic.py
@@ -138,31 +138,36 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
 
     _LOGGER.info("Looper version: {}\nCommand: {}".format(__version__, subcommand_name))
 
-    looper_cfg_path = os.path.relpath(dotfile_path(), start=os.curdir)
-
-    try:
-        if subcommand_args.looper_config:
-            looper_config_dict = read_looper_config_file(subcommand_args.looper_config)
-        else:
-            looper_config_dict = read_looper_dotfile()
-            _LOGGER.info(f"Using looper config ({looper_cfg_path}).")
-
-        sample_modifiers_dict = None
-        cli_modifiers_dict = None
-        for looper_config_key, looper_config_item in looper_config_dict.items():
-            if looper_config_key == SAMPLE_MODS_KEY:
-                sample_modifiers_dict = looper_config_item
-            elif looper_config_key == CLI_MODS_KEY:
-                cli_modifiers_dict = looper_config_item
+    if subcommand_args.config_file is None:
+        looper_cfg_path = os.path.relpath(dotfile_path(), start=os.curdir)
+        try:
+            if subcommand_args.looper_config:
+                looper_config_dict = read_looper_config_file(
+                    subcommand_args.looper_config
+                )
             else:
-                setattr(subcommand_args, looper_config_key, looper_config_item)
-
-    except OSError:
-        parser.print_help(sys.stderr)
+                looper_config_dict = read_looper_dotfile()
+                _LOGGER.info(f"Using looper config ({looper_cfg_path}).")
+
+            cli_modifiers_dict = None
+            for looper_config_key, looper_config_item in looper_config_dict.items():
+                if looper_config_key == CLI_KEY:
+                    cli_modifiers_dict = looper_config_item
+                else:
+                    setattr(subcommand_args, looper_config_key, looper_config_item)
+
+        except OSError:
+            parser.print_help(sys.stderr)
+            _LOGGER.warning(
+                f"Looper config file does not exist. Use looper init to create one at {looper_cfg_path}."
+            )
+            sys.exit(1)
+    else:
         _LOGGER.warning(
-            f"Looper config file does not exist. Use looper init to create one at {looper_cfg_path}."
+            "This PEP configures looper through the project config. This approach is deprecated and will "
+            "be removed in future versions. Please use a looper config file. For more information see "
+            "looper.databio.org/en/latest/looper-config"
         )
-        sys.exit(1)
 
     subcommand_args = enrich_args_via_cfg(
         subcommand_name,
@@ -195,7 +200,6 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
                 amendments=subcommand_args.amend,
                 divcfg_path=divcfg,
                 runp=subcommand_name == "runp",
-                sample_modifiers=sample_modifiers_dict,
                 **{
                     attr: getattr(subcommand_args, attr)
                     for attr in CLI_PROJ_ATTRS
@@ -211,7 +215,6 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
                 amendments=subcommand_args.amend,
                 divcfg_path=divcfg,
                 runp=subcommand_name == "runp",
-                sample_modifiers=sample_modifiers_dict,
                 project_dict=PEPHubClient()._load_raw_pep(
                     registry_path=subcommand_args.config_file
                 ),
diff --git a/looper/const.py b/looper/const.py
index e38cee18..de080260 100644
--- a/looper/const.py
+++ b/looper/const.py
@@ -93,7 +93,6 @@
     "DEBUG_EIDO_VALIDATION",
     "LOOPER_GENERIC_OUTPUT_SCHEMA",
     "LOOPER_GENERIC_COUNT_LINES",
-    "CLI_MODS_KEY",
     "PipelineLevel",
 ]
 
@@ -224,8 +223,6 @@ def _get_apperance_dict(type, templ=APPEARANCE_BY_FLAG):
 SAMPLE_PL_ARG = "sample_pipeline_interfaces"
 PROJECT_PL_ARG = "project_pipeline_interfaces"
 
-CLI_MODS_KEY = "cli_modifiers"
-
 
 DEFAULT_CFG_PATH = os.path.join(os.getcwd(), LOOPER_DOTFILE_NAME)
 CLI_PROJ_ATTRS = [
diff --git a/looper/project.py b/looper/project.py
index 6daecac1..7a652db7 100644
--- a/looper/project.py
+++ b/looper/project.py
@@ -131,19 +131,6 @@ def __init__(self, cfg=None, amendments=None, divcfg_path=None, **kwargs):
         except NotImplementedError:
             self.name = None
 
-        # consolidate sample modifiers
-        if kwargs.get(SAMPLE_MODS_KEY) and self._modifier_exists():
-            _LOGGER.warning(
-                "Sample modifiers were provided in Looper Config and in PEP Project Config. Merging..."
-            )
-            deep_update(self.config["sample_modifiers"], kwargs.get(SAMPLE_MODS_KEY))
-            _LOGGER.debug(
-                msg=f"Merged sample modifiers: {self.config['sample_modifiers']}"
-            )
-        elif kwargs.get(SAMPLE_MODS_KEY):
-            self.config.setdefault("sample_modifiers", {})
-            self.config["sample_modifiers"] = kwargs.get(SAMPLE_MODS_KEY)
-
         # add sample pipeline interface to the project
         if kwargs.get(SAMPLE_PL_ARG):
             self.set_sample_piface(kwargs.get(SAMPLE_PL_ARG))
diff --git a/looper/utils.py b/looper/utils.py
index 26776db7..4eb8ca4b 100644
--- a/looper/utils.py
+++ b/looper/utils.py
@@ -283,6 +283,8 @@ def enrich_args_via_cfg(
             if getattr(parser_args, key, None):
                 new_value = getattr(parser_args, key)
                 cfg_args_all[key] = new_value
+    else:
+        cfg_args_all = {}
 
     looper_config_cli_modifiers = None
     if cli_modifiers:
@@ -604,8 +606,8 @@ def read_looper_config_file(looper_config_path: str) -> dict:
     if SAMPLE_MODS_KEY in dp_data:
         return_dict[SAMPLE_MODS_KEY] = dp_data[SAMPLE_MODS_KEY]
 
-    if CLI_MODS_KEY in dp_data:
-        return_dict[CLI_MODS_KEY] = dp_data[CLI_MODS_KEY]
+    if CLI_KEY in dp_data:
+        return_dict[CLI_KEY] = dp_data[CLI_KEY]
 
     if PIPELINE_INTERFACES_KEY in dp_data: