diff --git a/alphadia/cli.py b/alphadia/cli.py
index 599276b5..8d3e86d1 100644
--- a/alphadia/cli.py
+++ b/alphadia/cli.py
@@ -16,14 +16,18 @@
 
 import alphadia
 from alphadia import utils
+from alphadia.constants.keys import ConfigKeys
 from alphadia.exceptions import CustomError
 from alphadia.search_plan import SearchPlan
 from alphadia.workflow import reporting
 
 logger = logging.getLogger()
 
+epilog = "Parameters passed via CLI will overwrite parameters from config file (except for  '--file': will be merged)."
 
-parser = argparse.ArgumentParser(description="Search DIA experiments with alphaDIA")
+parser = argparse.ArgumentParser(
+    description="Search DIA experiments with alphaDIA", epilog=epilog
+)
 parser.add_argument(
     "--version",
     "-v",
@@ -32,17 +36,19 @@
 )
 parser.add_argument(
     "--output",
+    "--output-directory",
     "-o",
     type=str,
-    help="Output directory",
+    help="Output directory.",
     nargs="?",
     default=None,
 )
 parser.add_argument(
     "--file",
+    "--raw-path",
     "-f",
     type=str,
-    help="Raw data input files.",
+    help="Path to raw data input file. Can be passed multiple times.",
     action="append",
     default=[],
 )
@@ -58,21 +64,23 @@
     "--regex",
     "-r",
     type=str,
-    help="Regex to match raw files in directory.",
+    help="Regex to match raw files in 'directory'.",
     nargs="?",
     default=".*",
 )
 parser.add_argument(
     "--library",
+    "--library-path",
     "-l",
     type=str,
-    help="Spectral library.",
+    help="Path to spectral library file.",
     nargs="?",
     default=None,
 )
 parser.add_argument(
     "--fasta",
-    help="Fasta file(s) used to generate or annotate the spectral library.",
+    "--fasta-path",
+    help="Path to fasta file used to generate or annotate the spectral library. Can be passed multiple times.",
     action="append",
     default=[],
 )
@@ -80,21 +88,22 @@
     "--config",
     "-c",
     type=str,
-    help="Config yaml which will be used to update the default config.",
+    help="Path to config yaml file which will be used to update the default config.",
     nargs="?",
     default=None,
 )
 parser.add_argument(
     "--config-dict",
     type=str,
-    help="Python Dict which will be used to update the default config.",
+    help="Python dictionary which will be used to update the default config.",
     nargs="?",
     default="{}",
 )
 parser.add_argument(
-    "--quant-dir",
+    "--quant-dir",  # TODO deprecate
+    "--quant-directory",
     type=str,
-    help="Directory to save the quantification results (psm & frag parquet files) to be reused in a distributed search",
+    help="Directory to save the quantification results (psm & frag parquet files) to be reused in a distributed search.",
     nargs="?",
     default=None,
 )
@@ -148,7 +157,7 @@ def _get_raw_path_list_from_args_and_config(
         list: a list of file paths that match the specified regex pattern.
     """
 
-    raw_path_list = config.get("raw_path_list", [])
+    raw_path_list = config.get(ConfigKeys.RAW_PATHS, [])
     raw_path_list += args.file
 
     if (config_directory := config.get("directory")) is not None:
@@ -172,17 +181,6 @@ def _get_raw_path_list_from_args_and_config(
     return raw_path_list
 
 
-def _get_fasta_list_from_args_and_config(
-    args: argparse.Namespace, config: dict
-) -> list:
-    """Parse fasta file list from command line arguments and config file, merging them if both are given."""
-
-    fasta_path_list = config.get("fasta_list", [])
-    fasta_path_list += args.fasta
-
-    return fasta_path_list
-
-
 def run(*args, **kwargs):
     # parse command line arguments
     args, unknown = parser.parse_known_args()
@@ -203,18 +201,23 @@ def run(*args, **kwargs):
     )
     if output_directory is None:
         parser.print_help()
-        print("No output directory specified.")
+
+        print("No output directory specified. Please do so via CL-argument or config.")
         return
     reporting.init_logging(output_directory)
 
-    quant_dir = _get_from_args_or_config(
-        args, user_config, args_key="quant_dir", config_key="quant_dir"
-    )
-    raw_path_list = _get_raw_path_list_from_args_and_config(args, user_config)
-    library_path = _get_from_args_or_config(
-        args, user_config, args_key="library", config_key="library"
-    )
-    fasta_path_list = _get_fasta_list_from_args_and_config(args, user_config)
+    # TODO revisit the multiple sources of raw files (cli, config, regex, ...)
+    raw_paths = _get_raw_path_list_from_args_and_config(args, user_config)
+    cli_params_config = {
+        **({ConfigKeys.RAW_PATHS: raw_paths} if raw_paths else {}),
+        **({ConfigKeys.LIBRARY_PATH: args.library} if args.library is not None else {}),
+        **({ConfigKeys.FASTA_PATHS: args.library} if args.fasta else {}),
+        **(
+            {ConfigKeys.QUANT_DIRECTORY: args.library}
+            if args.quant_dir is not None
+            else {}
+        ),
+    }
 
     # TODO rename all output_directory, output_folder => output_path, quant_dir->quant_path (except cli parameter)
 
@@ -222,14 +225,7 @@ def run(*args, **kwargs):
     matplotlib.use("Agg")
 
     try:
-        SearchPlan(
-            output_directory,
-            raw_path_list=raw_path_list,
-            library_path=library_path,
-            fasta_path_list=fasta_path_list,
-            config=user_config,
-            quant_path=quant_dir,
-        ).run_plan()
+        SearchPlan(output_directory, user_config, cli_params_config).run_plan()
 
     except Exception as e:
         if isinstance(e, CustomError):
diff --git a/alphadia/constants/default.yaml b/alphadia/constants/default.yaml
index 7b44c78b..2276518e 100644
--- a/alphadia/constants/default.yaml
+++ b/alphadia/constants/default.yaml
@@ -1,10 +1,12 @@
 # configuration for the extraction plan
 version: 1
 
-library: null
+# These values are typically filled via CLI parameters
 output_directory: null
-raw_path_list: []
-output: null
+library_path: null
+raw_paths: []
+fasta_paths: []
+quant_directory: null
 
 general:
   thread_count: 10
@@ -63,31 +65,31 @@ library_prediction:
 #    composition: H(-2)2H(8)13C(2)
 custom_modifications:
   # Dimethyl @K channel decoy
-  Dimethyl:d12@K:
+  - name: Dimethyl:d12@K
     composition: H(-2)2H(8)13C(2)
 
   # Dimethyl @Any_N-term channel decoy
-  Dimethyl:d12@Any_N-term:
+  - name: Dimethyl:d12@Any_N-term
     composition: H(-2)2H(8)13C(2)
 
   # Dimethyl @Protein_N-term channel decoy
-  Dimethyl:d12@Protein_N-term:
+  - name: Dimethyl:d12@Protein_N-term
     composition: H(-2)2H(8)13C(2)
 
   # mTRAQ @K channel decoy
-  mTRAQ:d12@K:
+  - name: mTRAQ:d12@K
     composition: H(12)C(1)13C(10)15N(2)O(1)
 
   # mTRAQ @Any_N-term channel decoy
-  mTRAQ:d12@Any_N-term:
+  - name: mTRAQ:d12@Any_N-term
     composition: H(12)C(1)13C(14)15N(2)O(1)
 
   # mTRAQ @Protein_N-term channel decoy
-  mTRAQ:d12@Protein_N-term:
+  - name: mTRAQ:d12@Protein_N-term
     composition: H(12)C(1)13C(14)15N(2)O(1)
 
   # SILAC heavy @K channel decoy
-  Label:13C(12)@K:
+  - name: Label:13C(12)@K
     composition: C(12)
 
 search:
diff --git a/alphadia/constants/keys.py b/alphadia/constants/keys.py
index 1f786966..1b3f04da 100644
--- a/alphadia/constants/keys.py
+++ b/alphadia/constants/keys.py
@@ -22,3 +22,13 @@ class StatOutputKeys(metaclass=ConstantsClass):
     MS2_ERROR = "ms2_error"
     RT_ERROR = "rt_error"
     MOBILITY_ERROR = "mobility_error"
+
+
+class ConfigKeys(metaclass=ConstantsClass):
+    """String constants for accessing the config."""
+
+    OUTPUT_DIRECTORY = "output_directory"
+    LIBRARY_PATH = "library_path"
+    RAW_PATHS = "raw_paths"
+    FASTA_PATHS = "fasta_paths"
+    QUANT_DIRECTORY = "quant_directory"
diff --git a/alphadia/constants/multistep.yaml b/alphadia/constants/multistep.yaml
index 1bfbeb38..c1c3875d 100644
--- a/alphadia/constants/multistep.yaml
+++ b/alphadia/constants/multistep.yaml
@@ -12,6 +12,7 @@ transfer:
     enabled: True
 
   # override settings that could have been set by the user:
+  quant_directory: null
   general:
     save_library: False
     reuse_quant: False
@@ -23,6 +24,7 @@ library:
 #    predict: True
 
   # override settings that could have been set by the user:
+  quant_directory: null
   general:
     save_library: False
     reuse_quant: False
@@ -37,6 +39,7 @@ mbr:
   search:
     target_num_candidates: 5
   # override settings that could have been set by the user:
+  quant_directory: null
   general:
     reuse_quant: False
   library_prediction:
diff --git a/alphadia/exceptions.py b/alphadia/exceptions.py
index 94efbc7e..e8f93131 100644
--- a/alphadia/exceptions.py
+++ b/alphadia/exceptions.py
@@ -20,6 +20,9 @@ def msg(self):
     def detail_msg(self):
         return self._detail_msg
 
+    def __str__(self):
+        return f"{self._error_code}: {self._msg} {self._detail_msg}"
+
 
 class BusinessError(CustomError):
     """Custom error class for 'business' errors.
@@ -59,3 +62,33 @@ class NotDiaDataError(BusinessError):
     _error_code = "NOT_DIA_DATA"
 
     _msg = "Could not find cycle shape. Please check if this is a valid DIA data set."
+
+
+class ConfigError(BusinessError):
+    """Raise when something is wrong with the provided configuration."""
+
+    _error_code = "CONFIG_ERROR"
+
+    _msg = "Malformed configuration file(s)."
+    _key = ""
+    _config_name = ""
+
+    def __init__(self, key: str, config_name: str):
+        self._key = key
+        self._config_name = config_name
+
+
+class KeyAddedConfigError(ConfigError):
+    """Raise when a key should be added to a config."""
+
+    def __init__(self, key: str, config_name: str):
+        super().__init__(key, config_name)
+        self._detail_msg = f"Defining new keys is not allowed when updating a config: key='{self._key}', config_name='{self._config_name}'"
+
+
+class TypeMismatchConfigError(ConfigError):
+    """Raise when the type of a value does not match the default type."""
+
+    def __init__(self, key: str, config_name: str, extra_msg: str):
+        super().__init__(key, config_name)
+        self._detail_msg = f"Types of values must match default config: key='{self._key}', config_name='{self._config_name}', types='{extra_msg}'"
diff --git a/alphadia/libtransform.py b/alphadia/libtransform.py
index 805b4073..08a475f4 100644
--- a/alphadia/libtransform.py
+++ b/alphadia/libtransform.py
@@ -40,10 +40,10 @@ def __call__(self, *args: typing.Any) -> typing.Any:
             return self.forward(*args)
         else:
             logger.critical(
-                f"Input {input} failed validation for {self.__class__.__name__}"
+                f"Input {args} failed validation for {self.__class__.__name__}"
             )
             raise ValueError(
-                f"Input {input} failed validation for {self.__class__.__name__}"
+                f"Input {args} failed validation for {self.__class__.__name__}"
             )
 
     def validate(self, *args: typing.Any) -> bool:
diff --git a/alphadia/search_plan.py b/alphadia/search_plan.py
index 2d065d8a..ef8dc5cb 100644
--- a/alphadia/search_plan.py
+++ b/alphadia/search_plan.py
@@ -8,7 +8,7 @@
 import pandas as pd
 import yaml
 
-from alphadia.constants.keys import StatOutputKeys
+from alphadia.constants.keys import ConfigKeys, StatOutputKeys
 from alphadia.outputtransform import (
     SearchPlanOutput,
 )
@@ -34,11 +34,8 @@ class SearchPlan:
     def __init__(
         self,
         output_directory: str,
-        raw_path_list: list[str],
-        library_path: str | None,
-        fasta_path_list: list[str],
-        config: dict,
-        quant_dir: str | None,
+        config: dict | None = None,
+        cli_params_config: dict | None = None,
     ):
         """Initialize search plan.
 
@@ -48,40 +45,27 @@ def __init__(
 
         Parameters
         ----------
-        config:
-            User configuration.
         output_directory:
             Output directory.
-        library_path:
-            Library path.
-        fasta_path_list:
-            List of fasta paths.
-        quant_dir:
-            Quantification directory holding previous results.
-        raw_path_list
-            List of raw paths.
+        config:
+            Configuration provided by user (loaded from file and/or dictionary)
+        cli_params_config
+            config-like dictionary of parameters directly provided by CLI
         """
-
-        self._user_config: dict = config
-        self._output_dir: Path = Path(output_directory)
         reporting.init_logging(output_directory)
 
-        self._library_path: Path | None = (
-            None if library_path is None else Path(library_path)
+        self._output_dir: Path = Path(output_directory)
+        self._user_config: dict = config if config is not None else {}
+        self._cli_params_config: dict = (
+            cli_params_config if cli_params_config is not None else {}
         )
-        self._fasta_path_list: list[str] = fasta_path_list
-        self._raw_path_list: list[str] = raw_path_list
 
         # these are the default paths if the library step is the only one
         self._library_step_output_dir: Path = self._output_dir
-        self._library_quant_dir: Path | None = (
-            None if quant_dir is None else Path(quant_dir)
-        )
 
         # multistep search:
         self._multistep_config: dict | None = None
         self._transfer_step_output_dir: Path | None = None
-        self._mbr_step_library_path: Path | None = None
 
         multistep_search_config = self._user_config.get("multistep_search", {})
         self._transfer_step_enabled = multistep_search_config.get(
@@ -107,16 +91,11 @@ def _update_paths(self) -> None:
 
         # in case transfer step is enabled, we need to adjust the library step settings
         if self._transfer_step_enabled:
-            self._library_quant_dir = None
             self._transfer_step_output_dir = self._output_dir / TRANSFER_STEP_NAME
 
         # in case mbr step is enabled, we need to adjust the library step settings
         if self._mbr_step_enabled:
-            self._library_quant_dir = None
             self._library_step_output_dir = self._output_dir / LIBRARY_STEP_NAME
-            self._mbr_step_library_path = (
-                self._library_step_output_dir / f"{SearchPlanOutput.LIBRARY_OUTPUT}.hdf"
-            )
 
     def run_plan(self):
         """Run the search plan.
@@ -127,8 +106,6 @@ def run_plan(self):
         print_logo()
         print_environment()
 
-        # TODO add some logging here on the directories (if they are not logged elsewhere)
-
         extra_config_for_library_step = (
             self._multistep_config[LIBRARY_STEP_NAME]
             if self._transfer_step_enabled or self._mbr_step_enabled
@@ -142,7 +119,6 @@ def run_plan(self):
             # output: DL model
             self.run_step(
                 self._transfer_step_output_dir,
-                self._library_path,
                 self._multistep_config[TRANSFER_STEP_NAME],
             )
 
@@ -170,9 +146,7 @@ def run_plan(self):
         logger.info(f"Running step '{LIBRARY_STEP_NAME}'")
         self.run_step(
             self._library_step_output_dir,
-            self._library_path,
             extra_config_for_library_step,
-            self._library_quant_dir,
         )
 
         if self._mbr_step_enabled:
@@ -183,31 +157,31 @@ def run_plan(self):
                     self._library_step_output_dir
                 )
 
+            mbr_step_library_path = str(
+                self._library_step_output_dir / f"{SearchPlanOutput.LIBRARY_OUTPUT}.hdf"
+            )
+
             mbr_step_extra_config = (
-                self._multistep_config[MBR_STEP_NAME] | optimized_values_config
+                self._multistep_config[MBR_STEP_NAME]
+                | optimized_values_config
+                | {ConfigKeys.LIBRARY_PATH: mbr_step_library_path}
             )
             self.run_step(
                 self._output_dir,
-                self._mbr_step_library_path,
                 mbr_step_extra_config,
             )
 
     def run_step(
         self,
         output_directory: Path,
-        library_path: Path | None,
         extra_config: dict,
-        quant_dir: Path | None = None,
     ) -> None:
         """Run a single step of the search plan."""
         step = SearchStep(
             output_folder=str(output_directory),
-            raw_path_list=self._raw_path_list,
-            library_path=None if library_path is None else str(library_path),
-            fasta_path_list=self._fasta_path_list,
             config=self._user_config,
+            cli_config=self._cli_params_config,
             extra_config=extra_config,
-            quant_path=None if quant_dir is None else str(quant_dir),
         )
         step.run()
 
diff --git a/alphadia/search_step.py b/alphadia/search_step.py
index 959b7c5e..c109ae0d 100644
--- a/alphadia/search_step.py
+++ b/alphadia/search_step.py
@@ -9,10 +9,16 @@
 from alphabase.spectral_library.flat import SpecLibFlat
 
 from alphadia import libtransform, outputtransform
+from alphadia.constants.keys import ConfigKeys
 from alphadia.exceptions import CustomError
 from alphadia.workflow import peptidecentric, reporting
 from alphadia.workflow.base import WorkflowBase
-from alphadia.workflow.config import MULTISTEP_SEARCH, USER_DEFINED, Config
+from alphadia.workflow.config import (
+    MULTISTEP_SEARCH,
+    USER_DEFINED,
+    USER_DEFINED_CLI_PARAM,
+    Config,
+)
 
 SPECLIB_FILE_NAME = "speclib.hdf"
 
@@ -23,13 +29,10 @@ class SearchStep:
     def __init__(
         self,
         output_folder: str,
-        raw_path_list: list[str] | None = None,
-        library_path: str | None = None,
-        fasta_path_list: list[str] | None = None,
         config: dict | Config | None = None,
-        config_base_path: str | None = None,
+        cli_config: dict | None = None,
         extra_config: dict | None = None,
-        quant_path: str | None = None,
+        config_base_path: str | None = None,
     ) -> None:
         """Highest level class to plan a DIA search step.
 
@@ -42,53 +45,34 @@ def __init__(
         output_folder : str
             output folder to save the results
 
-        raw_path_list : list
-            list of input file locations
-
-        library_path : str, optional
-            path to the spectral library file. If not provided, the library is built from fasta files
-
-        fasta_path_list : list, optional
-            list of fasta file locations to build the library from
-
-        config_base_path : str, optional
-            user-provided yaml file containing the default config.
-
         config : dict, optional
-            user-provided dict to update the default config. Can be used for debugging purposes etc.
+            values to update the default config. Overrides values in `default.yaml` and `config_base_path`.
 
-        extra_config : dict, optional
-            dict to update the final config. Used for multistep searches.
+        cli_config : dict, optional
+            additional config values (parameters from the command line). Overrides values in `config`.
 
-        quant_path : str, optional
-            path to directory to save the quantification results (psm & frag parquet files). If not provided, the results are saved in the usual workflow folder
+        extra_config : dict, optional
+            additional config values (parameters to orchestrate multistep searches). Overrides values in `config` and `cli_config`.
 
+        config_base_path : str, optional
+            absolute path to yaml file containing additional config values. Overrides values in `default.yaml`.
         """
 
-        if config is None:
-            config = {}
-        if fasta_path_list is None:
-            fasta_path_list = []
-        if raw_path_list is None:
-            raw_path_list = []
-
         self.output_folder = output_folder
         os.makedirs(output_folder, exist_ok=True)
         reporting.init_logging(self.output_folder)
 
-        self.raw_path_list = raw_path_list
-        self.library_path = library_path
-        self.fasta_path_list = fasta_path_list
-        self.quant_path = quant_path
-
-        self.spectral_library = None
-
         self._config = self._init_config(
-            config, extra_config, output_folder, config_base_path
+            config, cli_config, extra_config, output_folder, config_base_path
         )
-
         logger.setLevel(logging.getLevelName(self._config["general"]["log_level"]))
 
+        self.raw_path_list = self._config[ConfigKeys.RAW_PATHS]
+        self.library_path = self._config[ConfigKeys.LIBRARY_PATH]
+        self.fasta_path_list = self._config[ConfigKeys.FASTA_PATHS]
+
+        self.spectral_library = None
+
         self.init_alphabase()
         self.load_library()
 
@@ -96,48 +80,64 @@ def __init__(
 
         self._log_inputs()
 
+    @staticmethod
     def _init_config(
-        self,
-        user_config: dict | Config,
-        extra_config: dict,
+        user_config: dict | Config | None,
+        cli_config: dict | None,
+        extra_config: dict | None,
         output_folder: str,
         config_base_path: str | None,
     ) -> Config:
         """Initialize the config with default values and update with user defined values."""
 
-        # default config path is not defined in the function definition to account for different path separators on different OS
-        if config_base_path is None:
-            # default yaml config location under /misc/config/config.yaml
-            config_base_path = os.path.join(
-                os.path.dirname(__file__), "constants", "default.yaml"
-            )
-
-        logger.info(f"loading config from {config_base_path}")
+        default_config_path = os.path.join(
+            os.path.dirname(__file__), "constants", "default.yaml"
+        )
+        logger.info(f"loading config from {default_config_path}")
         config = Config()
-        config.from_yaml(config_base_path)
+        config.from_yaml(default_config_path)
 
         config_updates = []
-        # load update config from dict
-        if isinstance(user_config, dict):
-            user_config_update = Config(USER_DEFINED)
-            user_config_update.from_dict(user_config)
-            config_updates.append(user_config_update)
-        elif isinstance(user_config, Config):
-            config_updates.append(user_config)
-        else:
-            raise ValueError("'config' parameter must be of type 'dict' or 'Config'")
-
+        if config_base_path is not None:
+            logger.info(f"loading additional config from {config_base_path}")
+            user_config_from_file = Config(USER_DEFINED)
+            user_config_from_file.from_yaml(default_config_path)
+            config_updates.append(user_config_from_file)
+
+        if user_config is not None:
+            logger.info("loading additional config provided via CLI")
+            # load update config from dict
+            if isinstance(user_config, dict):
+                user_config_update = Config(USER_DEFINED)
+                user_config_update.from_dict(user_config)
+                config_updates.append(user_config_update)
+            elif isinstance(user_config, Config):
+                config_updates.append(user_config)
+            else:
+                raise ValueError(
+                    "'config' parameter must be of type 'dict' or 'Config'"
+                )
+
+        if cli_config is not None:
+            logger.info("loading additional config provided via CLI parameters")
+            cli_config_update = Config(USER_DEFINED_CLI_PARAM)
+            cli_config_update.from_dict(cli_config)
+            config_updates.append(cli_config_update)
+
+        # this needs to be last
         if extra_config is not None:
             extra_config_update = Config(MULTISTEP_SEARCH)
             extra_config_update.from_dict(extra_config)
-            # need to overwrite user-defined output folder here
-            extra_config["output"] = output_folder
+            # need to overwrite user-defined output folder here to have correct value in config dump
+            extra_config[ConfigKeys.OUTPUT_DIRECTORY] = output_folder
             config_updates.append(extra_config_update)
 
         config.update(config_updates, do_print=True)
 
-        if "output" not in config:
-            config["output"] = output_folder
+        if ConfigKeys.OUTPUT_DIRECTORY not in config:
+            config[ConfigKeys.OUTPUT_DIRECTORY] = output_folder
+
+        config.to_yaml(os.path.join(output_folder, "frozen_config.yaml"))
 
         return config
 
@@ -162,12 +162,14 @@ def spectral_library(self, spectral_library: SpecLibFlat) -> None:
     def init_alphabase(self):
         """Init alphabase by registering custom modifications."""
 
-        # register custom modifications
-        if "custom_modifications" in self.config:
-            n_modifications = len(self.config["custom_modifications"])
-            logging.info(f"Registering {n_modifications} custom modifications")
+        new_modifications = {}
+        for mod in self.config["custom_modifications"]:
+            new_modifications[mod["name"]] = {"composition": mod["composition"]}
+
+        if new_modifications:
+            logging.info(f"Registering {len(new_modifications)} custom modifications")
 
-            modification.add_new_modifications(self.config["custom_modifications"])
+            modification.add_new_modifications(new_modifications)
 
     def load_library(self):
         """
@@ -340,7 +342,7 @@ def _process_raw_file(
         workflow = peptidecentric.PeptideCentricWorkflow(
             raw_name,
             self.config,
-            quant_path=self.quant_path,
+            quant_path=self.config["quant_directory"],
         )
 
         # check if the raw file is already processed
diff --git a/alphadia/workflow/base.py b/alphadia/workflow/base.py
index 02aff0e1..b9a9e726 100644
--- a/alphadia/workflow/base.py
+++ b/alphadia/workflow/base.py
@@ -5,6 +5,8 @@
 # alpha family imports
 from alphabase.spectral_library.base import SpecLibBase
 
+from alphadia.constants.keys import ConfigKeys
+
 # alphadia imports
 from alphadia.data import alpharaw_wrapper, bruker
 from alphadia.workflow import manager, reporting
@@ -52,7 +54,7 @@ def __init__(
         """
         self._instance_name: str = instance_name
         self._parent_path: str = quant_path or os.path.join(
-            config["output"], QUANT_FOLDER_NAME
+            config[ConfigKeys.OUTPUT_DIRECTORY], QUANT_FOLDER_NAME
         )
         logger.info(f"Saving quantification results to {self._parent_path}")
 
diff --git a/alphadia/workflow/config.py b/alphadia/workflow/config.py
index 55d7a1f3..a59b9c92 100644
--- a/alphadia/workflow/config.py
+++ b/alphadia/workflow/config.py
@@ -15,10 +15,13 @@
 
 import yaml
 
+from alphadia.exceptions import KeyAddedConfigError, TypeMismatchConfigError
+
 logger = logging.getLogger()
 
 DEFAULT = "default"
 USER_DEFINED = "user defined"
+USER_DEFINED_CLI_PARAM = "user defined (cli)"
 MULTISTEP_SEARCH = "multistep search"
 
 
@@ -100,7 +103,10 @@ def _recursive_defaultdict():
         tracking_dict = defaultdict(_recursive_defaultdict)
 
         current_config = deepcopy(self.config)
+
         for config in configs:
+            logger.info(f"Updating config with '{config.name}'")
+
             _update(
                 current_config,
                 config.to_dict(),
@@ -169,14 +175,12 @@ def _update(
 
     Raises
     ------
-    ValueError in these cases:
-    - a key is not found in the target_config
-    - the type of the update value does not match the type of the target value
-    - an item is not found in the target_config
+    - KeyAddedConfigError: a key is not found in the target_config
+    - ValueTypeMismatchConfigError: the type of the update value does not match the type of the target value
     """
     for key, update_value in update_config.items():
         if key not in target_config:
-            raise ValueError(f"Key not found in target_config: '{key}'")
+            raise KeyAddedConfigError(key, config_name)
 
         target_value = target_config[key]
         tracking_value = tracking_dict[key]
@@ -189,8 +193,8 @@ def _update(
                 and isinstance(update_value, int | float)
             )
         ):
-            raise ValueError(
-                f"Type mismatch for key '{key}': {type(update_value)} != {type(target_value)}"
+            raise TypeMismatchConfigError(
+                key, config_name, f"{type(update_value)} != {type(target_value)}"
             )
 
         if isinstance(target_value, dict):
diff --git a/docs/guides/transfer-dimethyl.md b/docs/guides/transfer-dimethyl.md
index e9804e4a..d5a61968 100644
--- a/docs/guides/transfer-dimethyl.md
+++ b/docs/guides/transfer-dimethyl.md
@@ -153,3 +153,7 @@ multistep_search:
   transfer_step_enabled: True
   mbr_step_enabled: True
 ```
+
+In case the multistep search fails at some step, you can restart the failed step by
+using the `full_config.yaml` that is stored in the respective subfolder. You can of course edit
+this file in order to fix the issue that caused the failure.
diff --git a/gui/src/main/modules/workflows.js b/gui/src/main/modules/workflows.js
index cb671b75..ffd7b344 100644
--- a/gui/src/main/modules/workflows.js
+++ b/gui/src/main/modules/workflows.js
@@ -79,15 +79,15 @@ function workflowToConfig(workflow) {
     let output = {name: workflow.name}
 
     if (workflow.library.path != "") {
-        output["library"] = workflow.library.path
+        output["library_path"] = workflow.library.path
     }
 
     if (workflow.fasta_list.path != "") {
-        output["fasta_list"] = workflow.fasta_list.path
+        output["fasta_paths"] = workflow.fasta_list.path
     }
 
     if (workflow.raw_path_list.path != "") {
-        output["raw_path_list"] = workflow.raw_path_list.path
+        output["raw_paths"] = workflow.raw_path_list.path
     }
 
     if (workflow.output_directory.path != "") {
diff --git a/misc/distributed_search/parse_parameters.py b/misc/distributed_search/parse_parameters.py
index 476013e5..27c8f283 100755
--- a/misc/distributed_search/parse_parameters.py
+++ b/misc/distributed_search/parse_parameters.py
@@ -58,7 +58,7 @@ def safe_add_key(config, parent_key, key, value):
 safe_add_key(config, "library_prediction", "predict", False)
 
 # remove any fasta if one is present in the config file
-config.pop("fasta_list", None)
+config.pop("fasta_paths", None)
 
 # determine chunk size: division of infile rowcount and number of nodes
 chunk_size = int(np.ceil(infile.shape[0] / int(args.nnodes)))
@@ -79,7 +79,7 @@ def safe_add_key(config, parent_key, key, value):
 
     # save current chunk indices into chunk-yaml as raw files
     safe_add_key(
-        current_config, None, "raw_path_list", list(all_filepaths[start_idx:end_idx])
+        current_config, None, "raw_paths", list(all_filepaths[start_idx:end_idx])
     )
 
     # create folder for current chunk in target directory. Don't create the folder if it already exists.
@@ -99,7 +99,7 @@ def safe_add_key(config, parent_key, key, value):
         sys.exit(1)
 
     # set library path in config
-    safe_add_key(current_config, None, "library", lib_source)
+    safe_add_key(current_config, None, "library_path", lib_source)
 
     # set chunk folder as output_directory in the config
     safe_add_key(current_config, None, "output_directory", "./")
diff --git a/misc/distributed_search/speclib_config.py b/misc/distributed_search/speclib_config.py
index 0ad79e67..41e7b221 100755
--- a/misc/distributed_search/speclib_config.py
+++ b/misc/distributed_search/speclib_config.py
@@ -39,17 +39,17 @@ def safe_add_key(config, parent_key, key, value):
 # if library and fasta are set, predicting will result in repredicted & annotated library
 # add fasta_list to config
 _new_fasta_list = [args.fasta_path] if args.fasta_path else []
-safe_add_key(config, None, "fasta_list", _new_fasta_list)
+safe_add_key(config, None, "fasta_paths", _new_fasta_list)
 
 # add library path to config
 _new_library = args.library_path if args.library_path else None
-safe_add_key(config, None, "library", _new_library)
+safe_add_key(config, None, "library_path", _new_library)
 
 # set library prediction to True
 safe_add_key(config, "library_prediction", "predict", True)
 
 # remove rawfiles for prediction step in case some are set
-config.pop("raw_path_list", None)
+config.pop("raw_paths", None)
 
 # set output directory for predicted spectral library
 safe_add_key(config, None, "output_directory", os.path.join(args.target_directory))
diff --git a/tests/e2e_tests/e2e_test_cases.yaml b/tests/e2e_tests/e2e_test_cases.yaml
index 01698f0c..b46093b1 100644
--- a/tests/e2e_tests/e2e_test_cases.yaml
+++ b/tests/e2e_tests/e2e_test_cases.yaml
@@ -24,10 +24,10 @@ test_cases:
         target_rt_tolerance: 100
       calibration:
         batch_size: 1000
-    library:
+    library_path:
 #      - source_url: https://datashare.biochem.mpg.de/s/Uw2yfNSbApfPpTk # hela_hybrid.hdf
       - source_url: https://datashare.biochem.mpg.de/s/cNdrN4OJC9AAHhz # hela_hybrid.small.hdf
-    raw_data:
+    raw_paths:
       - source_url: https://datashare.biochem.mpg.de/s/339jg5HtGrwLwDN/download?files=20231017_OA2_TiHe_ADIAMA_HeLa_200ng_Evo011_21min_F-40_05.raw
 #      - source_url: https://datashare.biochem.mpg.de/s/339jg5HtGrwLwDN/download?files=20231017_OA2_TiHe_ADIAMA_HeLa_200ng_Evo011_21min_F-40_06.raw
 #      - source_url: https://datashare.biochem.mpg.de/s/339jg5HtGrwLwDN/download?files=20231017_OA2_TiHe_ADIAMA_HeLa_200ng_Evo011_21min_F-40_07.raw
@@ -57,9 +57,9 @@ test_cases:
         transfer_step_enabled: True
         mbr_step_enabled: True
     # dimethyl data (from tutorial)
-    fasta:
+    fasta_paths:
       - source_url: https://datashare.biochem.mpg.de/s/1GiKQSwlPf6YlMm/download?path=%2F&files=2024_01_12_human.fasta
-    raw_data:
+    raw_paths:
       - source_url: https://datashare.biochem.mpg.de/s/1GiKQSwlPf6YlMm/download?path=%2Fraw_data&files=20240408_OA1_Evo12_31min_TiHe_SA_H032_E32_F-40_B1.raw
       - source_url: https://datashare.biochem.mpg.de/s/1GiKQSwlPf6YlMm/download?path=%2Fraw_data&files=20240408_OA1_Evo12_31min_TiHe_SA_H032_E32_F-40_B2.raw
       - source_url: https://datashare.biochem.mpg.de/s/1GiKQSwlPf6YlMm/download?path=%2Fraw_data&files=20240408_OA1_Evo12_31min_TiHe_SA_H032_E32_F-40_B3.raw
@@ -85,9 +85,9 @@ test_cases:
       search_output:
         peptide_level_lfq: true
         precursor_level_lfq: true
-    library:
+    library_path:
       - source_url: https://datashare.biochem.mpg.de/s/e4jqILnxHPujBBP/download?files=MSFragger_library_60SPD_2.tsv
-    raw_data:
+    raw_paths:
       - source_url: https://datashare.biochem.mpg.de/s/e4jqILnxHPujBBP/download?files=20231218_TIMS03_PaSk_SA_K562_syPASEF_200ng_var_IM0713_S1-E7_1_41539.d
       - source_url: https://datashare.biochem.mpg.de/s/e4jqILnxHPujBBP/download?files=20231218_TIMS03_PaSk_SA_K562_syPASEF_200ng_var_IM0713_S1-F1_1_41545.d
       - source_url: https://datashare.biochem.mpg.de/s/e4jqILnxHPujBBP/download?files=20231218_TIMS03_PaSk_SA_K562_syPASEF_200ng_var_IM0713_S1-F7_1_41551.d
@@ -120,9 +120,9 @@ test_cases:
       search_output:
         peptide_level_lfq: true
         precursor_level_lfq: true
-    fasta:
+    fasta_paths:
       - source_url: https://datashare.biochem.mpg.de/s/WTu3rFZHNeb3uG2/download?files=2024_01_12_human.fasta
-    raw_data:
+    raw_paths:
       - source_url: https://datashare.biochem.mpg.de/s/WTu3rFZHNeb3uG2/download?files=20231024_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_before_01.raw
       - source_url: https://datashare.biochem.mpg.de/s/WTu3rFZHNeb3uG2/download?files=20231024_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_before_02.raw
       - source_url: https://datashare.biochem.mpg.de/s/WTu3rFZHNeb3uG2/download?files=20231024_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_before_03.raw
@@ -156,9 +156,9 @@ test_cases:
       search_output:
         peptide_level_lfq: true
         precursor_level_lfq: true
-    fasta:
+    fasta_paths:
       - source_url: https://datashare.biochem.mpg.de/s/WTu3rFZHNeb3uG2/download?files=2024_01_12_human.fasta
-    raw_data:
+    raw_paths:
       - source_url: https://datashare.biochem.mpg.de/s/WTu3rFZHNeb3uG2/download?files=20231024_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_before_01.raw
       - source_url: https://datashare.biochem.mpg.de/s/WTu3rFZHNeb3uG2/download?files=20231024_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_before_02.raw
       - source_url: https://datashare.biochem.mpg.de/s/WTu3rFZHNeb3uG2/download?files=20231024_OA3_TiHe_ADIAMA_HeLa_200ng_Evo01_21min_F-40_iO_before_03.raw
@@ -191,9 +191,9 @@ test_cases:
 #      search_output:
 #        peptide_level_lfq: true
 #        precursor_level_lfq: true
-#    library:
+#    library_path:
 #      - source_url: https://datashare.biochem.mpg.de/s/Q9D8N2mq8vlzQ1f  #speclib.mbr.hdf
-#    raw_data:
+#    raw_paths:
 #      - source_url: ...
 #    metrics:
 #      - BasicStats
diff --git a/tests/e2e_tests/prepare_test_data.py b/tests/e2e_tests/prepare_test_data.py
index 4bc6a335..261e7c33 100644
--- a/tests/e2e_tests/prepare_test_data.py
+++ b/tests/e2e_tests/prepare_test_data.py
@@ -55,18 +55,18 @@ def _create_config_file(
     """Create the config file from paths to the input files and optional extra_config."""
 
     config_to_write = {
-        "raw_path_list": downloaded_files[YamlKeys.RAW_DATA],
+        "raw_paths": downloaded_files[YamlKeys.RAW_DATA],
         "output_directory": os.path.join(target_path, OUTPUT_DIR_NAME),
     } | extra_config
 
     if YamlKeys.LIBRARY in downloaded_files:
         config_to_write = config_to_write | {
-            "library": downloaded_files[YamlKeys.LIBRARY][0]
+            "library_path": downloaded_files[YamlKeys.LIBRARY][0]
         }
 
     if YamlKeys.FASTA in downloaded_files:
         config_to_write = config_to_write | {
-            "fasta_list": downloaded_files[YamlKeys.FASTA]
+            "fasta_paths": downloaded_files[YamlKeys.FASTA]
         }
 
     config_target_path = os.path.join(target_path, DEFAULT_CONFIG_FILE_NAME)
diff --git a/tests/unit_tests/test_config.py b/tests/unit_tests/test_config.py
index b7c71655..bdf4be82 100644
--- a/tests/unit_tests/test_config.py
+++ b/tests/unit_tests/test_config.py
@@ -4,6 +4,7 @@
 import pytest
 import yaml
 
+from alphadia.exceptions import KeyAddedConfigError, TypeMismatchConfigError
 from alphadia.workflow.config import Config
 
 generic_default_config = """
@@ -205,7 +206,7 @@ def test_config_update_new_key_raises():
     config_2.from_dict({"new_key": 0})
 
     # when
-    with pytest.raises(ValueError, match="Key not found in target_config: 'new_key'"):
+    with pytest.raises(KeyAddedConfigError):
         config_1.update([config_2], do_print=True)
 
 
@@ -219,8 +220,7 @@ def test_config_update_type_mismatch_raises():
 
     # when
     with pytest.raises(
-        ValueError,
-        match="Type mismatch for key 'simple_value_int': <class 'str'> != <class 'int'>",
+        TypeMismatchConfigError,
     ):
         config_1.update([config_2], do_print=True)
 
diff --git a/tests/unit_tests/test_search_plan.py b/tests/unit_tests/test_search_plan.py
index 9224df8f..2380ee7f 100644
--- a/tests/unit_tests/test_search_plan.py
+++ b/tests/unit_tests/test_search_plan.py
@@ -17,6 +17,13 @@
     "some_user_config_key": "some_user_config_value",
 }
 
+BASE_CLI_PARAMS_CONFIG = {
+    "raw_paths": ["/raw1"],
+    "library_path": "/user_provided_library_path",
+    "fasta_paths": ["/fasta1"],
+    "quant_directory": "/user_provided_quant_path",
+}
+
 
 def get_search_plan(config):
     """Helper function to create a SearchPlan object with a given config."""
@@ -25,11 +32,8 @@ def get_search_plan(config):
     ):
         return SearchPlan(
             output_directory="/user_provided_output_path",
-            raw_path_list=["/raw1"],
-            library_path="/user_provided_library_path",
-            fasta_path_list=["/fasta1"],
             config=config,
-            quant_dir="/user_provided_quant_path",
+            cli_params_config=BASE_CLI_PARAMS_CONFIG,
         )
 
 
@@ -47,12 +51,9 @@ def test_runs_plan_without_transfer_and_mbr_steps(mock_plan, mock_init_logging):
     # could use `mock_plan.assert_has_calls([call(..)])` pattern here but it is harder to read in case of error
     assert mock_plan.call_args_list[0].kwargs == {
         "output_folder": "/user_provided_output_path",
-        "raw_path_list": ["/raw1"],
-        "library_path": "/user_provided_library_path",
-        "fasta_path_list": ["/fasta1"],
         "config": BASE_USER_CONFIG,
         "extra_config": {},
-        "quant_path": "/user_provided_quant_path",
+        "cli_config": BASE_CLI_PARAMS_CONFIG,
     }
 
     mock_plan.return_value.run.assert_called_once_with()
@@ -66,12 +67,7 @@ def test_runs_plan_without_transfer_and_mbr_steps_none_dirs(
     """Test that the SearchPlan object runs the plan correctly without transfer and mbr steps when all parameters are none or empty."""
 
     search_plan = SearchPlan(
-        output_directory="/user_provided_output_path",
-        raw_path_list=[],
-        library_path=None,
-        fasta_path_list=[],
-        config={},
-        quant_dir=None,
+        output_directory="/user_provided_output_path", config={}, cli_params_config={}
     )
 
     # when
@@ -82,12 +78,9 @@ def test_runs_plan_without_transfer_and_mbr_steps_none_dirs(
     # could use `mock_plan.assert_has_calls([call(..)])` pattern here but it is harder to read in case of error
     assert mock_plan.call_args_list[0].kwargs == {
         "output_folder": "/user_provided_output_path",
-        "raw_path_list": [],
-        "library_path": None,
-        "fasta_path_list": [],
         "config": {},
         "extra_config": {},
-        "quant_path": None,
+        "cli_config": {},
     }
 
     mock_plan.return_value.run.assert_called_once_with()
@@ -120,20 +113,14 @@ def test_runs_plan_with_transfer_step(
     # transfer_step
     assert mock_plan.call_args_list[0].kwargs == {
         "output_folder": "/user_provided_output_path/transfer",
-        "raw_path_list": ["/raw1"],
-        "library_path": "/user_provided_library_path",
-        "fasta_path_list": ["/fasta1"],
         "config": BASE_USER_CONFIG | additional_user_config,
         "extra_config": MOCK_MULTISTEP_CONFIG["transfer"],
-        "quant_path": None,
+        "cli_config": BASE_CLI_PARAMS_CONFIG,
     }
 
     # library_step
     assert mock_plan.call_args_list[1].kwargs == {
         "output_folder": "/user_provided_output_path",
-        "raw_path_list": ["/raw1"],
-        "library_path": "/user_provided_library_path",
-        "fasta_path_list": ["/fasta1"],
         "config": BASE_USER_CONFIG | additional_user_config,
         "extra_config": MOCK_MULTISTEP_CONFIG["library"]
         | {
@@ -143,7 +130,7 @@ def test_runs_plan_with_transfer_step(
             },
         }
         | dynamic_config,
-        "quant_path": None,
+        "cli_config": BASE_CLI_PARAMS_CONFIG,
     }
 
     mock_plan.return_value.run.assert_has_calls([call(), call()])
@@ -177,23 +164,19 @@ def test_runs_plan_with_mbr_step(mock_get_dyn_config, mock_plan, mock_init_loggi
     # library_step
     assert mock_plan.call_args_list[0].kwargs == {
         "output_folder": "/user_provided_output_path/library",
-        "raw_path_list": ["/raw1"],
-        "library_path": "/user_provided_library_path",
-        "fasta_path_list": ["/fasta1"],
         "config": BASE_USER_CONFIG | additional_user_config,
         "extra_config": MOCK_MULTISTEP_CONFIG["library"],
-        "quant_path": None,
+        "cli_config": BASE_CLI_PARAMS_CONFIG,
     }
 
     # mbr_step
     assert mock_plan.call_args_list[1].kwargs == {
         "output_folder": "/user_provided_output_path",
-        "raw_path_list": ["/raw1"],
-        "library_path": "/user_provided_output_path/library/speclib.mbr.hdf",
-        "fasta_path_list": ["/fasta1"],
         "config": BASE_USER_CONFIG | additional_user_config,
-        "extra_config": MOCK_MULTISTEP_CONFIG["mbr"] | dynamic_config,
-        "quant_path": None,
+        "extra_config": MOCK_MULTISTEP_CONFIG["mbr"]
+        | dynamic_config
+        | {"library_path": "/user_provided_output_path/library/speclib.mbr.hdf"},
+        "cli_config": BASE_CLI_PARAMS_CONFIG,
     }
 
     mock_plan.return_value.run.assert_has_calls([call(), call()])
@@ -229,20 +212,14 @@ def test_runs_plan_with_transfer_and_mbr_steps(
     # transfer_step
     assert mock_plan.call_args_list[0].kwargs == {
         "output_folder": "/user_provided_output_path/transfer",
-        "raw_path_list": ["/raw1"],
-        "library_path": "/user_provided_library_path",
-        "fasta_path_list": ["/fasta1"],
         "config": BASE_USER_CONFIG | additional_user_config,
         "extra_config": MOCK_MULTISTEP_CONFIG["transfer"],
-        "quant_path": None,
+        "cli_config": BASE_CLI_PARAMS_CONFIG,
     }
 
     # library_step
     assert mock_plan.call_args_list[1].kwargs == {
         "output_folder": "/user_provided_output_path/library",
-        "raw_path_list": ["/raw1"],
-        "library_path": "/user_provided_library_path",
-        "fasta_path_list": ["/fasta1"],
         "config": BASE_USER_CONFIG | additional_user_config,
         "extra_config": MOCK_MULTISTEP_CONFIG["library"]
         | {
@@ -252,18 +229,19 @@ def test_runs_plan_with_transfer_and_mbr_steps(
             },
         }
         | dynamic_config,
-        "quant_path": None,
+        "cli_config": BASE_CLI_PARAMS_CONFIG,
     }
 
     # mbr_step
     assert mock_plan.call_args_list[2].kwargs == {
         "output_folder": "/user_provided_output_path",
-        "raw_path_list": ["/raw1"],
-        "library_path": "/user_provided_output_path/library/speclib.mbr.hdf",
-        "fasta_path_list": ["/fasta1"],
         "config": BASE_USER_CONFIG | additional_user_config,
-        "extra_config": MOCK_MULTISTEP_CONFIG["mbr"] | dynamic_config,
-        "quant_path": None,
+        "extra_config": MOCK_MULTISTEP_CONFIG["mbr"]
+        | dynamic_config
+        | {
+            "library_path": "/user_provided_output_path/library/speclib.mbr.hdf",
+        },
+        "cli_config": BASE_CLI_PARAMS_CONFIG,
     }
 
     mock_plan.return_value.run.assert_has_calls([call(), call(), call()])
diff --git a/tests/unit_tests/test_search_step.py b/tests/unit_tests/test_search_step.py
index 63d75a80..61ee0b47 100644
--- a/tests/unit_tests/test_search_step.py
+++ b/tests/unit_tests/test_search_step.py
@@ -17,8 +17,8 @@ def test_fasta_digest():
     tempdir = tempfile.gettempdir()
     step = search_step.SearchStep(
         tempdir,
-        fasta_path_list=[common_contaminants],
         config={"library_prediction": {"predict": True}},
+        cli_config={"fasta_paths": [common_contaminants]},
     )
 
     assert len(step.spectral_library.precursor_df) > 0
@@ -30,8 +30,8 @@ def test_fasta_digest():
     # predict existing library
     step = search_step.SearchStep(
         tempdir,
-        library_path=speclib_path,
         config={"library_prediction": {"predict": True}},
+        cli_config={"library_path": speclib_path},
     )
     assert len(step.spectral_library.precursor_df) > 0
     assert len(step.spectral_library.fragment_df) > 0
@@ -39,8 +39,8 @@ def test_fasta_digest():
     # load existing library without predict
     step = search_step.SearchStep(
         tempdir,
-        library_path=speclib_path,
         config={"library_prediction": {"predict": False}},
+        cli_config={"library_path": speclib_path},
     )
     assert len(step.spectral_library.precursor_df) > 0
     assert len(step.spectral_library.fragment_df) > 0
@@ -68,10 +68,13 @@ def test_library_loading():
     for test_dict in test_cases:
         print("Testing {}".format(test_dict["name"]))
 
+        # TODO this is not a unit test
         test_data_location = DataShareDownloader(
             test_dict["url"], temp_directory
         ).download()
-        step = search_step.SearchStep(temp_directory, library_path=test_data_location)
+        step = search_step.SearchStep(
+            temp_directory, {"library_path": test_data_location}
+        )
         assert len(step.spectral_library.precursor_df) > 0
         assert len(step.spectral_library.fragment_df) > 0
 
@@ -81,12 +84,13 @@ def test_custom_modifications():
     temp_directory = tempfile.gettempdir()
 
     config = {
-        "custom_modifications": {
-            "ThisModDoesNotExists@K": {
+        "custom_modifications": [
+            {
+                "name": "ThisModDoesNotExists@K",
                 "composition": "H(10)",
             },
-        }
+        ]
     }
 
-    step = search_step.SearchStep(temp_directory, [], config=config)  # noqa F841
+    step = search_step.SearchStep(temp_directory, config=config)  # noqa F841
     assert "ThisModDoesNotExists@K" in MOD_DF["mod_name"].values
diff --git a/tests/unit_tests/test_workflow.py b/tests/unit_tests/test_workflow.py
index 807c5518..d297b1e8 100644
--- a/tests/unit_tests/test_workflow.py
+++ b/tests/unit_tests/test_workflow.py
@@ -307,7 +307,7 @@ def test_workflow_base():
             with open(config_path) as f:
                 config = yaml.safe_load(f)
 
-            config["output"] = tempfile.gettempdir()
+            config["output_directory"] = tempfile.gettempdir()
 
             workflow_name = Path(file).stem
 
@@ -317,10 +317,10 @@ def test_workflow_base():
             )
             my_workflow.load(file, pd.DataFrame({}))
 
-            assert my_workflow.config["output"] == config["output"]
+            assert my_workflow.config["output_directory"] == config["output_directory"]
             assert my_workflow.instance_name == workflow_name
             assert my_workflow.parent_path == os.path.join(
-                config["output"], base.QUANT_FOLDER_NAME
+                config["output_directory"], base.QUANT_FOLDER_NAME
             )
             assert my_workflow.path == os.path.join(
                 my_workflow.parent_path, workflow_name
@@ -420,7 +420,7 @@ def create_workflow_instance():
 
     config = Config()
     config.from_yaml(config_base_path)
-    config["output"] = tempfile.mkdtemp()
+    config["output_directory"] = tempfile.mkdtemp()
     workflow = peptidecentric.PeptideCentricWorkflow(
         "test",
         config,