diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 00000000..f8f438a2
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,20 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: NF1-CellPainting-Data-Repository
+message: NF1 dataset repository
+type: dataset
+authors:
+  - given-names: Jenna
+    family-names: Tomkinson
+  - given-names: Greg
+    family-names: Way
+identifiers:
+  - type: url
+    value: >-
+      https://github.com/WayScience/nf1_cellpainting_data/tree/main
+    description: Github repository of the dataset
+repository-code: >-
+  https://github.com/WayScience/nf1_cellpainting_data/tree/main
+license: CC0-1.0
diff --git a/all_cellprofiler.sqlite b/all_cellprofiler.sqlite
deleted file mode 120000
index 39247b71..00000000
--- a/all_cellprofiler.sqlite
+++ /dev/null
@@ -1 +0,0 @@
-/home/erikserrano/Development/NF1_SchwannCell_data/CellProfiler_pipelines/Analysis_Output/Plate1_Output/all_cellprofiler.sqlite
\ No newline at end of file
diff --git a/cytosnake/tests/functional/datasets/emptyfiles/metadata/platemap/platemap1.csv b/cytosnake/tests/functional/datasets/emptyfiles/metadata/platemap/platemap1.csv
deleted file mode 100644
index e69de29b..00000000
diff --git a/cytosnake/tests/functional/datasets/emptyfiles/metadata/platemap/platemap2.csv b/cytosnake/tests/functional/datasets/emptyfiles/metadata/platemap/platemap2.csv
deleted file mode 100644
index e69de29b..00000000
diff --git a/cytosnake/tests/functional/datasets/emptyfiles/plate_data1.sqlite b/cytosnake/tests/functional/datasets/emptyfiles/plate_data1.sqlite
deleted file mode 100644
index e69de29b..00000000
diff --git a/cytosnake/tests/functional/datasets/emptyfiles/plate_data2.sqlite b/cytosnake/tests/functional/datasets/emptyfiles/plate_data2.sqlite
deleted file mode 100644
index e69de29b..00000000
diff --git a/cytosnake/tests/functional/test_cli.py b/cytosnake/tests/functional/test_cli.py
deleted file mode 100644
index 2e7ab625..00000000
--- a/cytosnake/tests/functional/test_cli.py
+++ /dev/null
@@ -1,226 +0,0 @@
-"""
-module: test_cli.py
-
-This testing module composes of functional tests that contains checks for both positive
-negative cases when using CytoSnake's CLI
-
-A positive case indicates that given the user parameters we expect it to run
-successfully.
-
-A negative case indicates that given with the user parameters, our tests are able to
-capture the errors.
-
-Ultimately, test_cli.py will contains functional test to all modes that CytoSnake
-contains.
-"""
-
-import os
-import pathlib
-import shutil
-import subprocess
-from typing import Optional
-
-from cytosnake.common import errors
-
-
-# -----------------
-# Helper functions
-# -----------------
-class CleanUpHandler:
-    """Used to clean up directories in every single test run"""
-
-    def __init__(self, tmp_path):
-        self.tmp_path = tmp_path
-
-    def __call__(self) -> None:
-        shutil.rmtree(self.tmp_path)
-
-
-def transfer_data(
-    test_dir: pathlib.Path,
-    n_plates: int,
-    n_platemaps: int,
-    metadata_dir_name: Optional[str] = "metadata",
-    testing_data_dir="emptyfiles",
-) -> None:
-    """Wrapper function that transfer datasets found within the pytest module and
-    transfers it to the assigned directory where pytest is conducting the functional
-    tests.
-
-    The test dataset is transfered from the `dataset` directory located in the
-    same directory as the functional test module. The dataset directory contains
-    empty files that emulates inputs that a user will put in to CytoSnake.
-
-    Parameters
-    ----------
-    test_dir : pathlib.Path
-        testing directory
-
-    n_plates: int
-        number of plates
-
-    n_platesmaps: int
-        number of plate maps
-
-    metadata_dir_name : Optional[str]
-        name of the metadata directory (default=metadata)
-
-    Return
-    ------
-    None
-        Transfers datafiles from the PyTest module to the testing directory
-    """
-
-    # get files to transfer
-    # dataset folder is within the same directory as the test modules, changes
-    # in this path will cause the tests to fail
-    dataset_dir = pathlib.Path(f"./datasets/{testing_data_dir}").resolve(strict=True)
-
-    # grabbing all input paths
-    sqlite_file_paths = list(dataset_dir.glob("*sqlite"))[:n_plates]
-    platemaps_dir = dataset_dir / "metadata" / "platemap"
-    plate_map_files = [
-        str(_path.absolute()) for _path in platemaps_dir.glob("platemap*")
-    ][:n_platemaps]
-    barcode = dataset_dir / "barcode.txt"
-
-    # create a metadata_dir in tmp_dir
-    if not isinstance(metadata_dir_name, str):
-        raise ValueError("metadata dir name must be a string")
-
-    tmpdir_metadata_path = test_dir / metadata_dir_name / "platemap"
-    tmpdir_metadata_path.mkdir(exist_ok=True, parents=True)
-
-    # transferring all files to tmp dir
-    for _path in plate_map_files:
-        shutil.copy(_path, str(tmpdir_metadata_path))
-    for _path in sqlite_file_paths:
-        shutil.copy(_path, test_dir)
-    shutil.copy(barcode, test_dir)
-
-
-def get_raised_error(traceback: str) -> str:
-    """Parses traceback and attempts to obtain raised exception error.
-
-    Traceback is parsed in this order:
-    1. split by new lines
-    2. grab the last line as it contains the raised exception and message
-    3. split by ":" to separate exception name and exception message
-    4. grab the first element since it contains that path to exception
-    5. split by "." and grab last element, which is the exception name
-
-    Parameters
-    ----------
-    traceback : str
-        complete traceback generated by executing CLI
-
-    Returns
-    -------
-    str
-        return raised exception error
-    """
-
-    # returns exception name, refer to function documentation to understand
-    # the order of parsing the traceback to obtain exception name.
-    return traceback.splitlines()[-1].split(":")[0].split(".")[-1]
-
-
-# --------------------------
-# init mode functional tests
-# --------------------------
-# The tests below focuses on only executing the init mode.
-def test_barcode_logic_no_barcode_one_platemap(tmp_path, request) -> None:
-    """Positive case: This tests expects a successful run where the user provides
-    multiple plate datasets, plate map, and no barcode. Since this is only one plate_map
-    , this means that the generated dataset came from one experiment and multiple
-    samples (plates) were used to generated the datasets.
-    """
-    # starting path
-    test_module = str(pathlib.Path().absolute())
-
-    # transfer placeholder data to tmpdir
-    transfer_data(test_dir=tmp_path, n_plates=2, n_platemaps=1)
-
-    # change directory to tmpdir
-    os.chdir(tmp_path)
-
-    # execute CytoSnake
-    cmd = "cytosnake init -d *.sqlite -m metadata".split()
-    proc = subprocess.run(cmd, capture_output=True, text=True, check=False)
-
-    # leave test directory
-    os.chdir(test_module)
-
-    # clean directory,
-    cleanup_handler = CleanUpHandler(tmp_path)
-    request.addfinalizer(cleanup_handler)
-
-    # checking for success return code
-    assert proc.returncode == 0
-
-
-def test_barcode_logic_barcode_multi_platemaps(tmp_path, request) -> None:
-    """Positive case: This tests expects a successful run where the user provides
-    multiple plate datasets, multiple plate map, and barcode. Since this is only one
-    plate_map , this means that the generated dataset came from one experiment and
-    multiple samples (plates) were used to generated the datasets.
-    """
-    # PyTest module directory
-    test_module = str(pathlib.Path().absolute())
-
-    # transfer placeholder data to tmpdir
-    transfer_data(test_dir=tmp_path, n_plates=2, n_platemaps=2)
-
-    # change directory to tmpdir
-    os.chdir(tmp_path)
-
-    # execute CytoSnake
-    cmd = "cytosnake init -d *.sqlite -m metadata -b barcode.txt".split()
-    proc = subprocess.run(cmd, capture_output=True, text=True, check=False)
-
-    # leave testing dir
-    os.chdir(test_module)
-
-    # clean directory,
-    cleanup_handler = CleanUpHandler(tmp_path)
-    request.addfinalizer(cleanup_handler)
-
-    # checking for success return code
-    assert proc.returncode == 0
-
-
-def test_barcode_logic_no_barcode_multi_platemaps(tmp_path, request) -> None:
-    """Negative case: This test expects a failed run where the user provides multiple
-    plate datasets, multiple plate maps (multi-experiments), and no barcode. Since
-    there are plate maps, this indicates that the generated datasets came from multiple
-    experiments.
-
-    Checks:
-    -------
-        non-zero return code
-        BarCodeRequiredError raised
-    """
-    # PyTest module directory
-    test_module = str(pathlib.Path().absolute())
-
-    # transfer placeholder data to tmpdir
-    transfer_data(test_dir=tmp_path, n_plates=2, n_platemaps=2)
-
-    # change directory to tmpdir
-    os.chdir(tmp_path)
-
-    # execute CytoSnake
-    cmd = "cytosnake init -d *.sqlite -m metadata"
-    proc = subprocess.run(cmd, shell=True, capture_output=True, text=True, check=False)
-    raised_error = get_raised_error(proc.stderr)
-
-    # leave testing dir
-    os.chdir(test_module)
-
-    # clean directory,
-    cleanup_handler = CleanUpHandler(tmp_path)
-    request.addfinalizer(cleanup_handler)
-
-    # checking for success return code
-    assert proc.returncode == 1
-    assert raised_error == errors.BarcodeRequiredError.__name__
diff --git a/cytosnake/utils/test_utils.py b/cytosnake/utils/test_utils.py
new file mode 100644
index 00000000..807ff16f
--- /dev/null
+++ b/cytosnake/utils/test_utils.py
@@ -0,0 +1,230 @@
+"""
+module: test_utils.py
+
+test_utils.py contain additional functions that enhance testing capabilities, providing
+extra functionality for conducting comprehensive and robust tests.
+"""
+import os
+import pathlib
+import shutil
+from dataclasses import dataclass
+from typing import Optional
+
+import cytosnake
+
+# setting test root folder path
+TEST_ROOT_PATH = pathlib.Path(cytosnake.__path__[0]).parent / "tests"
+
+
+@dataclass
+class DataFiles:
+    """Structured datatype representation that contains all files in a selected dataset
+
+    Attributes:
+    -----------
+    metadata: str | list[str]
+        metadata directory name
+    plate_data: list[str]
+        list of plate data (parquet or sqlite files)
+    barcode : str
+        barcode file name
+
+    Returns
+    -------
+    DataFiles
+        DataStructure representation of test dataset files
+    """
+
+    # required parameters
+    dataset_dir: str | pathlib.Path
+
+    # extracted files
+    metadata: str | list[str] = None
+    plate_data: str | list[str] = None
+    barcode: str = None
+
+    # extracting file paths and setting into dataclass attributes
+    def __post_init__(self):
+        self._extract_content_files()
+
+    def _extract_content_files(self):
+        """extracts all files within given dataset folder and sets the DataFile
+        dataclass attributes
+
+        Raises
+        ------
+        TypeError
+            raised if dataset_dir is not a str or pathlib.Path object.
+            raised if plate data is not parquet or sqlite file
+        """
+        # get all top level files
+        if not isinstance(self.dataset_dir, (str, pathlib.Path)):
+            raise TypeError("dataset_dir must be a string or pathlib.Path object")
+        if isinstance(self.dataset_dir, str):
+            self.dataset_dir = pathlib.Path(self.dataset_dir).resolve(strict=True)
+
+        # get all files
+        all_files = list(self.dataset_dir.glob("*"))
+
+        # get data files
+        plate_data = [
+            str(fpath.name)
+            for fpath in all_files
+            if any(fpath.suffix == ext for ext in [".parquet", ".sqlite"])
+        ]
+        self.plate_data = plate_data
+
+        # get metadata_dir
+        meta_data_path = [str(fpath.name) for fpath in all_files if fpath.is_dir()]
+        self.metadata = (
+            meta_data_path[0] if len(meta_data_path) == 1 else meta_data_path
+        )
+
+        # get barcode
+        barcode_path = [
+            str(fpath.name)
+            for fpath in all_files
+            if any(fpath.suffix == ext for ext in [".txt", ".csv"])
+        ]
+        self.barcode = (
+            (barcode_path[0] if len(barcode_path) == 1 else barcode_path)
+            if len(barcode_path) > 0
+            else None
+        )
+
+
+def get_raised_error(traceback: str) -> str:
+    """Parses traceback and attempts to obtain raised exception error.
+
+    Traceback is parsed in this order:
+    1. split by new lines
+    2. grab the last line as it contains the raised exception and message
+    3. split by ":" to separate exception name and exception message
+    4. grab the first element since it contains that path to exception
+    5. split by "." and grab last element, which is the exception name
+
+    Parameters
+    ----------
+    traceback : str
+        complete traceback generated by executing CLI
+
+    Returns
+    -------
+    str
+        name of raised exception error
+    """
+
+    # returns exception name, refer to function documentation to understand
+    # the order of parsing the traceback to obtain exception name.
+    return traceback.splitlines()[-1].split(":")[0].split(".")[-1]
+
+
+def get_test_data_folder(test_data_name: str) -> DataFiles:
+    """Gets single or multiple datasets. Users provide the name of the datasets
+    that will be used in their tests
+
+    Parameters/home/axiom/Projects/CytoSnake/cytosnake/utils/datasets
+        name or names of datasets to be selected
+
+    Returns
+    -------
+    DataFiles
+        contains all files in a dataclass format
+
+    Raises:
+    -------
+    FileNotFoundError
+        Raised when the provided test_data_name is not a valid testing dataset.
+    """
+
+    # type checking
+    if not isinstance(test_data_name, str):
+        raise TypeError("`test_data_name` must be a string")
+
+    # get testing dataset_path
+    data_dir_path = (TEST_ROOT_PATH / "datasets").resolve(strict=True)
+    sel_test_data = (data_dir_path / test_data_name).resolve(strict=True)
+
+    # convert to DataFiles content
+    data_files = DataFiles(sel_test_data)
+
+    return data_files
+
+
+def prepare_dataset(
+    test_data_name: str,
+    test_dir_path: pathlib.Path,
+) -> DataFiles:
+    """Main function to prepare dataset into testing datafolder.
+
+    Parameters
+    ----------
+    test_data_name : str
+        name of the testing dataset you want to use
+
+    test_dir_path : pathlib.Path
+        path to testing directory
+
+    Returns
+    -------
+    DataFiles
+        Structured data object that contains all the files within the selected dataset
+    """
+    # get dataset and transfer to testing directory
+    datafiles = get_test_data_folder(test_data_name=test_data_name)
+    shutil.copytree(datafiles.dataset_dir, str(test_dir_path), dirs_exist_ok=True)
+
+    # change directory to the testing directory
+    os.chdir(str(test_dir_path))
+
+    return datafiles
+
+
+def check_init_outputs(
+    paths: DataFiles,
+    test_dir: pathlib.Path,
+    plate_data_ext: Optional[str] = "sqlite",
+):
+    """verifies if all the files are generated after executing a sucessfull `init` mode
+    run with CytoSnake.
+
+    Parameters
+    ----------
+    paths : test_utils.DataFiles
+        DataFile datastructure that contains all file inputs
+    test_dir : pathlib.Path
+        Path where the test is taken place
+    plate_data_ext : Optional[str], optional
+        plate data format, by default "sqlite"
+    """
+    # typpe checking
+    if not isinstance(paths, DataFiles):
+        raise TypeError(f"`paths` must be a DataFiles type, not: {type(paths)}")
+    if not isinstance(test_dir, pathlib.Path):
+        raise TypeError(
+            f"`test_dir` must be a pathlib.Path type, not: {type(test_dir)}"
+        )
+    if not isinstance(test_dir, pathlib.Path):
+        raise TypeError(
+            f"`plate_data_ext` must be a str type, not: {type(plate_data_ext)}"
+        )
+
+    # creating the paths to check
+    data_folder = test_dir / "data"
+    cytosnake_file = test_dir / ".cytosnake"
+    metadata_in_datafolder = data_folder / paths.metadata
+    all_plates = list(data_folder.glob("*.sqlite"))
+
+    # if the barcode is not None, get the path to barcode and check
+    if paths.barcode is not None:
+        barcodes_in_datafolder = data_folder / paths.barcode
+        print(paths.barcode)
+        assert barcodes_in_datafolder.exists()
+
+    # assert checks
+    assert data_folder.exists()
+    assert cytosnake_file.exists()
+    assert metadata_in_datafolder.exists()
+    assert all(
+        [str(plate_data).endswith(f".{plate_data_ext}") for plate_data in all_plates]
+    )
diff --git a/docs/cytosnake.cli.md b/docs/cytosnake.cli.md
index f79263d3..d90ea59e 100644
--- a/docs/cytosnake.cli.md
+++ b/docs/cytosnake.cli.md
@@ -55,6 +55,8 @@ cytosnake.cli.exec
    :show-inheritance:
 ```
 
+## Module contents
+
 ```{eval-rst}
 .. automodule:: cytosnake.cli
    :members:
diff --git a/docs/cytosnake.md b/docs/cytosnake.md
index 325185db..4c90ae26 100644
--- a/docs/cytosnake.md
+++ b/docs/cytosnake.md
@@ -8,6 +8,7 @@
 cytosnake.cli
 cytosnake.common
 cytosnake.guards
+cytosnake.tests
 cytosnake.utils
 ```
 
diff --git a/docs/cytosnake.tests.md b/docs/cytosnake.tests.md
new file mode 100644
index 00000000..ee02c985
--- /dev/null
+++ b/docs/cytosnake.tests.md
@@ -0,0 +1,21 @@
+# cytosnake.tests package
+
+## Submodules
+
+## cytosnake.tests.test_utils module
+
+```{eval-rst}
+.. automodule:: cytosnake.tests.test_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+```
+
+## Module contents
+
+```{eval-rst}
+.. automodule:: cytosnake.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:
+```
diff --git a/pyproject.toml b/pyproject.toml
index 779b226e..3612181d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,4 +10,11 @@ all = true
 ignore = ["F821"]
 
 [tool.ruff.flake8-self]
-ignore-names = ["snakemake"]
\ No newline at end of file
+ignore-names = ["snakemake"]
+
+# pytest config
+[tool.pytest.ini_options]
+markers = [
+    "positive: marks for positive test",
+    "negative: marks for a negative test"
+]
\ No newline at end of file
diff --git a/cytosnake/tests/functional/datasets/emptyfiles/barcode.txt b/tests/__init__.py
similarity index 100%
rename from cytosnake/tests/functional/datasets/emptyfiles/barcode.txt
rename to tests/__init__.py
diff --git a/tests/datasets/nf1-data-nobarcode/Plate_1_nf1_analysis.sqlite b/tests/datasets/nf1-data-nobarcode/Plate_1_nf1_analysis.sqlite
new file mode 100644
index 00000000..c93d1eaa
--- /dev/null
+++ b/tests/datasets/nf1-data-nobarcode/Plate_1_nf1_analysis.sqlite
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b78d90ac5ef1444ea14a94d97c7c9635ab3053ca6b235b7b33a5e2729c41281f
+size 4956160
diff --git a/tests/datasets/nf1-data-nobarcode/metadata/platemap/platemap_NF1_plate1.csv b/tests/datasets/nf1-data-nobarcode/metadata/platemap/platemap_NF1_plate1.csv
new file mode 100644
index 00000000..fe49dd9e
--- /dev/null
+++ b/tests/datasets/nf1-data-nobarcode/metadata/platemap/platemap_NF1_plate1.csv
@@ -0,0 +1,9 @@
+WellRow,WellCol,well_position,gene_name,genotype
+C,6,C6,NF1,WT
+C,7,C7,NF1,Null
+D,6,D6,NF1,WT
+D,7,D7,NF1,Null
+E,6,E6,NF1,WT
+E,7,E7,NF1,Null
+F,6,F6,NF1,WT
+F,7,F7,NF1,Null
diff --git a/tests/datasets/nf1-data/Plate_1_nf1_analysis.sqlite b/tests/datasets/nf1-data/Plate_1_nf1_analysis.sqlite
new file mode 100644
index 00000000..c93d1eaa
--- /dev/null
+++ b/tests/datasets/nf1-data/Plate_1_nf1_analysis.sqlite
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b78d90ac5ef1444ea14a94d97c7c9635ab3053ca6b235b7b33a5e2729c41281f
+size 4956160
diff --git a/tests/datasets/nf1-data/Plate_2_nf1_analysis.sqlite b/tests/datasets/nf1-data/Plate_2_nf1_analysis.sqlite
new file mode 100644
index 00000000..c3e0d091
--- /dev/null
+++ b/tests/datasets/nf1-data/Plate_2_nf1_analysis.sqlite
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8091091d350d094833362d11708e789fb34c93c161028d1eb22d66b2b11d0e7c
+size 32083968
diff --git a/tests/datasets/nf1-data/Plate_3_nf1_analysis.sqlite b/tests/datasets/nf1-data/Plate_3_nf1_analysis.sqlite
new file mode 100644
index 00000000..3f35632b
--- /dev/null
+++ b/tests/datasets/nf1-data/Plate_3_nf1_analysis.sqlite
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1df7afdd2703383b0ff5b18e8d0db4d49b09ec979c6b968cd2885f5b97cbc7f0
+size 578424832
diff --git a/tests/datasets/nf1-data/Plate_3_prime_nf1_analysis.sqlite b/tests/datasets/nf1-data/Plate_3_prime_nf1_analysis.sqlite
new file mode 100644
index 00000000..3ba1953b
--- /dev/null
+++ b/tests/datasets/nf1-data/Plate_3_prime_nf1_analysis.sqlite
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ac74703724e3403e4695d5df077400eb3f4c1dbf72fbfbe9ab044e5d771ff04e
+size 466550784
diff --git a/tests/datasets/nf1-data/Plate_4_nf1_analysis.sqlite b/tests/datasets/nf1-data/Plate_4_nf1_analysis.sqlite
new file mode 100644
index 00000000..98cebece
--- /dev/null
+++ b/tests/datasets/nf1-data/Plate_4_nf1_analysis.sqlite
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9edaba3a3f39cb41466b518c20b484728c11bef3d66a01255d64b4453ba7d3a6
+size 233775104
diff --git a/tests/datasets/nf1-data/barcode_platemap.csv b/tests/datasets/nf1-data/barcode_platemap.csv
new file mode 100644
index 00000000..641723e9
--- /dev/null
+++ b/tests/datasets/nf1-data/barcode_platemap.csv
@@ -0,0 +1,6 @@
+Assay_Plate_Barcode,Plate_Map_Name
+Plate_1_nf1_analysis,platemap_NF1_plate1
+Plate_2_nf1_analysis,platemap_NF1_plate2
+Plate_3_nf1_analysis,platemap_NF1_plate3
+Plate_3_prime_nf1_analysis,platemap_NF1_plate3
+Plate_4_nf1_analysis,platemap_NF1_plate4
diff --git a/tests/datasets/nf1-data/metadata/platemap/platemap_NF1_plate1.csv b/tests/datasets/nf1-data/metadata/platemap/platemap_NF1_plate1.csv
new file mode 100644
index 00000000..fe49dd9e
--- /dev/null
+++ b/tests/datasets/nf1-data/metadata/platemap/platemap_NF1_plate1.csv
@@ -0,0 +1,9 @@
+WellRow,WellCol,well_position,gene_name,genotype
+C,6,C6,NF1,WT
+C,7,C7,NF1,Null
+D,6,D6,NF1,WT
+D,7,D7,NF1,Null
+E,6,E6,NF1,WT
+E,7,E7,NF1,Null
+F,6,F6,NF1,WT
+F,7,F7,NF1,Null
diff --git a/tests/datasets/nf1-data/metadata/platemap/platemap_NF1_plate2.csv b/tests/datasets/nf1-data/metadata/platemap/platemap_NF1_plate2.csv
new file mode 100644
index 00000000..ef724972
--- /dev/null
+++ b/tests/datasets/nf1-data/metadata/platemap/platemap_NF1_plate2.csv
@@ -0,0 +1,33 @@
+WellRow,WellCol,well_position,gene_name,genotype
+A,1,A1,NF1,WT
+A,6,A6,NF1,WT
+A,7,A7,NF1,Null
+A,12,A12,NF1,Null
+B,1,B1,NF1,WT
+B,6,B6,NF1,WT
+B,7,B7,NF1,Null
+B,12,B12,NF1,Null
+C,1,C1,NF1,WT
+C,6,C6,NF1,WT
+C,7,C7,NF1,Null
+C,12,C12,NF1,Null
+D,1,D1,NF1,WT
+D,6,D6,NF1,WT
+D,7,D7,NF1,Null
+D,12,D12,NF1,Null
+E,1,E1,NF1,WT
+E,6,E6,NF1,WT
+E,7,E7,NF1,Null
+E,12,E12,NF1,Null
+F,1,F1,NF1,WT
+F,6,F6,NF1,WT
+F,7,F7,NF1,Null
+F,12,F12,NF1,Null
+G,1,G1,NF1,WT
+G,6,G6,NF1,WT
+G,7,G7,NF1,Null
+G,12,G12,NF1,Null
+H,1,H1,NF1,WT
+H,6,H6,NF1,WT
+H,7,H7,NF1,Null
+H,12,H12,NF1,Null
diff --git a/tests/datasets/nf1-data/metadata/platemap/platemap_NF1_plate3.csv b/tests/datasets/nf1-data/metadata/platemap/platemap_NF1_plate3.csv
new file mode 100644
index 00000000..a694fe9f
--- /dev/null
+++ b/tests/datasets/nf1-data/metadata/platemap/platemap_NF1_plate3.csv
@@ -0,0 +1,73 @@
+WellRow,WellCol,well_position,gene_name,genotype,seed_density
+B,1,B1,NF1,WT,500
+C,1,C1,NF1,WT,500
+D,1,D1,NF1,WT,500
+E,1,E1,NF1,WT,500
+F,1,F1,NF1,WT,500
+G,1,G1,NF1,WT,500
+B,2,B2,NF1,WT,1000
+C,2,C2,NF1,WT,1000
+D,2,D2,NF1,WT,1000
+E,2,E2,NF1,WT,1000
+F,2,F2,NF1,WT,1000
+G,2,G2,NF1,WT,1000
+B,3,B3,NF1,WT,2000
+C,3,C3,NF1,WT,2000
+D,3,D3,NF1,WT,2000
+E,3,E3,NF1,WT,2000
+F,3,F3,NF1,WT,2000
+G,3,G3,NF1,WT,2000
+B,4,B4,NF1,WT,4000
+C,4,C4,NF1,WT,4000
+D,4,D4,NF1,WT,4000
+E,4,E4,NF1,WT,4000
+F,4,F4,NF1,WT,4000
+G,4,G4,NF1,WT,4000
+B,5,B5,NF1,HET,500
+C,5,C5,NF1,HET,500
+D,5,D5,NF1,HET,500
+E,5,E5,NF1,HET,500
+F,5,F5,NF1,HET,500
+G,5,G5,NF1,HET,500
+B,6,B6,NF1,HET,1000
+C,6,C6,NF1,HET,1000
+D,6,D6,NF1,HET,1000
+E,6,E6,NF1,HET,1000
+F,6,F6,NF1,HET,1000
+G,6,G6,NF1,HET,1000
+B,7,B7,NF1,HET,2000
+C,7,C7,NF1,HET,2000
+D,7,D7,NF1,HET,2000
+E,7,E7,NF1,HET,2000
+F,7,F7,NF1,HET,2000
+G,7,G7,NF1,HET,2000
+B,8,B8,NF1,HET,4000
+C,8,C8,NF1,HET,4000
+D,8,D8,NF1,HET,4000
+E,8,E8,NF1,HET,4000
+F,8,F8,NF1,HET,4000
+G,8,G8,NF1,HET,4000
+B,9,B9,NF1,Null,500
+C,9,C9,NF1,Null,500
+D,9,D9,NF1,Null,500
+E,9,E9,NF1,Null,500
+F,9,F9,NF1,Null,500
+G,9,G9,NF1,Null,500
+B,10,B10,NF1,Null,1000
+C,10,C10,NF1,Null,1000
+D,10,D10,NF1,Null,1000
+E,10,E10,NF1,Null,1000
+F,10,F10,NF1,Null,1000
+G,10,G10,NF1,Null,1000
+B,11,B11,NF1,Null,2000
+C,11,C11,NF1,Null,2000
+D,11,D11,NF1,Null,2000
+E,11,E11,NF1,Null,2000
+F,11,F11,NF1,Null,2000
+G,11,G11,NF1,Null,2000
+B,12,B12,NF1,Null,4000
+C,12,C12,NF1,Null,4000
+D,12,D12,NF1,Null,4000
+E,12,E12,NF1,Null,4000
+F,12,F12,NF1,Null,4000
+G,12,G12,NF1,Null,4000
diff --git a/tests/datasets/nf1-data/metadata/platemap/platemap_NF1_plate4.csv b/tests/datasets/nf1-data/metadata/platemap/platemap_NF1_plate4.csv
new file mode 100644
index 00000000..8d80538c
--- /dev/null
+++ b/tests/datasets/nf1-data/metadata/platemap/platemap_NF1_plate4.csv
@@ -0,0 +1,61 @@
+WellRow,WellCol,well_position,gene_name,genotype,seed_density,siRNA,RNAiMax,Concentration
+B,2,B2,NF1,WT,1000,None,0,0
+B,3,B3,NF1,WT,1000,Scramble,1,0.05
+B,4,B4,NF1,WT,1000,Scramble,1,0.005
+B,5,B5,NF1,WT,1000,None,0,0
+B,6,B6,NF1,WT,1000,Scramble,1,0.005
+B,7,B7,NF1,WT,1000,Scramble,1,0.05
+B,8,B8,NF1,WT,1000,None,0,0
+B,9,B9,NF1,WT,1000,Scramble,1,0.05
+B,10,B10,NF1,WT,1000,Scramble,1,0.005
+B,11,B11,NF1,WT,1000,None,1,0
+C,2,C2,NF1,Null,1000,None,0,0
+C,3,C3,NF1,WT,1000,NF1 Target 1,1,0.05
+C,4,C4,NF1,WT,1000,NF1 Target 1,1,0.005
+C,5,C5,NF1,Null,1000,None,0,0
+C,6,C6,NF1,WT,1000,NF1 Target 1,1,0.05
+C,7,C7,NF1,WT,1000,NF1 Target 1,1,0.005
+C,8,C8,NF1,Null,1000,None,0,0
+C,9,C9,NF1,WT,1000,NF1 Target 1,1,0.05
+C,10,C10,NF1,WT,1000,NF1 Target 1,1,0.005
+C,11,C11,NF1,WT,1000,None,1,0
+D,2,D2,NF1,Null,1000,None,0,0
+D,3,D3,NF1,WT,1000,NF1 Target 2,1,0.05
+D,4,D4,NF1,WT,1000,NF1 Target 2,1,0.005
+D,5,D5,NF1,Null,1000,None,0,0
+D,6,D6,NF1,WT,1000,NF1 Target 2,1,0.05
+D,7,D7,NF1,WT,1000,NF1 Target 2,1,0.005
+D,8,D8,NF1,Null,1000,None,0,0
+D,9,D9,NF1,WT,1000,NF1 Target 2,1,0.05
+D,10,D10,NF1,WT,1000,NF1 Target 2,1,0.005
+D,11,D11,NF1,WT,1000,None,1,0
+E,2,E2,NF1,WT,1000,Scramble,1,0.1
+E,3,E3,NF1,WT,1000,Scramble,1,0.01
+E,4,E4,NF1,WT,1000,Scramble,1,0.001
+E,5,E5,NF1,WT,1000,Scramble,1,0.1
+E,6,E6,NF1,WT,1000,Scramble,1,0.01
+E,7,E7,NF1,WT,1000,Scramble,1,0.001
+E,8,E8,NF1,WT,1000,Scramble,1,0.1
+E,9,E9,NF1,WT,1000,Scramble,1,0.01
+E,10,E10,NF1,WT,1000,Scramble,1,0.001
+E,11,E11,NF1,WT,1000,None,0,0
+F,2,F2,NF1,WT,1000,NF1 Target 1,1,0.1
+F,3,F3,NF1,WT,1000,NF1 Target 1,1,0.01
+F,4,F4,NF1,WT,1000,NF1 Target 1,1,0.001
+F,5,F5,NF1,WT,1000,NF1 Target 1,1,0.1
+F,6,F6,NF1,WT,1000,NF1 Target 1,1,0.01
+F,7,F7,NF1,WT,1000,NF1 Target 1,1,0.001
+F,8,F8,NF1,WT,1000,NF1 Target 1,1,0.1
+F,9,F9,NF1,WT,1000,NF1 Target 1,1,0.01
+F,10,F10,NF1,WT,1000,NF1 Target 1,1,0.001
+F,11,F11,NF1,Null,1000,None,0,0
+G,2,G2,NF1,WT,1000,NF1 Target 2,1,0.1
+G,3,G3,NF1,WT,1000,NF1 Target 2,1,0.01
+G,4,G4,NF1,WT,1000,NF1 Target 2,1,0.001
+G,5,G5,NF1,WT,1000,NF1 Target 2,1,0.1
+G,6,G6,NF1,WT,1000,NF1 Target 2,1,0.01
+G,7,G7,NF1,WT,1000,NF1 Target 2,1,0.001
+G,8,G8,NF1,WT,1000,NF1 Target 2,1,0.1
+G,9,G9,NF1,WT,1000,NF1 Target 2,1,0.01
+G,10,G10,NF1,WT,1000,NF1 Target 2,1,0.001
+G,11,G11,NF1,Null,1000,None,0,0
diff --git a/tests/functional/test_cli.py b/tests/functional/test_cli.py
new file mode 100644
index 00000000..46cb6323
--- /dev/null
+++ b/tests/functional/test_cli.py
@@ -0,0 +1,215 @@
+"""
+module: test_cli.py
+
+Description:
+
+The test_cli.py module is a crucial part of the CytoSnake project, responsible for
+conducting functional tests on CytoSnake's Command Line Interface (CLI). These tests aim
+to ensure that the CLI functions correctly, handling both positive and negative
+scenarios effectively.
+
+The purpose of this module is to verify that the CytoSnake CLI operates as expected and
+provides accurate results when interacting with various user parameters and modes. It
+validates that the CLI can handle different inputs, execute successfully in positive
+cases, and properly report errors in negative cases.
+
+The test scenarios are categorized into two main types:
+
+Positive Cases:
+These test cases validate the expected behavior of the CLI when
+provided with valid user parameters. The primary goal is to ensure that the CLI executes
+successfully without errors and produces the correct output.
+
+Negative Cases:
+These test cases simulate scenarios where invalid user parameters are provided.
+The objective is to confirm that the CLI can identify and handle errors appropriately,
+providing informative error messages to the user.
+"""
+
+import os
+import pathlib
+import shutil
+import subprocess
+
+import pytest
+
+from cytosnake.common import errors
+from cytosnake.utils import test_utils
+
+
+# ---------------
+# PyTest Fixtures
+# ---------------
+@pytest.fixture
+def testing_dir(tmp_path, request):
+    """Creates a testing directory
+
+    Note: Pytest will tear down tmp_path per test
+
+    Parameters
+    ----------
+    tmp_path : pytest.fixture
+        pytest default fixture value to be called when creating a temp dir.
+
+    request : pytest.fixture
+        Allows custom testing function to be added in the testing workflow
+
+    returns:
+    --------
+    pathlib.Path
+        Path pointing to temporary directory
+    """
+    # setting paths
+    original_cwd = str(pathlib.Path(".").absolute())
+
+    # creating a temporary path
+    test_name = request.node.name
+    tmp_dir = (tmp_path / test_name).absolute()
+    tmp_dir.mkdir()
+
+    # return the temporary directory path
+    yield tmp_dir
+
+    # teardown: remove the testing
+    if os.path.exists(tmp_dir):
+        shutil.rmtree(tmp_dir)
+
+    #  change the current working directory to the oroginal root
+    os.chdir(str(original_cwd))
+
+
+# ---------------
+# Init Mode Tests
+# ---------------
+@pytest.mark.negative
+def test_multiplate_maps_no_barcode(testing_dir) -> None:
+    """Negative case test: Expects `BarcodeMissingError` and Non-zero return code
+
+    This tests checks if the CLI raises an error when a user provides multiple platemaps
+    but no barcodes.
+
+    Rational:
+    ---------
+        CytoSnake relies on a barcode file to accurately map each platemap to its
+        corresponding plate. If users provide multiple platemaps without a barcode,
+        it becomes impossible for CytoSnake to determine the correct association between
+        platemaps and their respective plates.
+
+    Parameters:
+    -----------
+    testing_dir: pytest.fixture
+        Testing directory
+    """
+
+    # transfer data to testing folder
+    test_utils.prepare_dataset(test_data_name="nf1-data", test_dir_path=testing_dir)
+
+    # Grab raised exception
+    with pytest.raises(subprocess.CalledProcessError) as subproc_error:
+        # execute test
+        proc = subprocess.run(
+            "cytosnake init -d *.sqlite -m metadata".split(),
+            capture_output=True,
+            text=True,
+            check=True,
+        )
+
+        # parse trace back generated from CytoSnake
+        raised_exception = test_utils.get_raised_error(proc.stderr)
+
+        # assert checking
+        assert subproc_error.value.returncode == 1
+        assert raised_exception == errors.BarcodeMissingError.__name__
+
+
+@pytest.mark.postive
+def test_one_plate_one_platemap(testing_dir) -> None:
+    """Positive case test: Expects a 0 exit code
+
+    This test checks if the CLI can handle one plate and one plate map without barcode
+    as inputs.
+
+    Rational:
+    ---------
+        As this input involves only one plate, CytoSnake does not require the process
+        of identifying which platemap corresponds to that plate.
+
+    Parameters:
+    -----------
+    test_dir: pytest.fixture
+        Testing directory
+    """
+
+    # prepare testing files
+    datafiles = test_utils.prepare_dataset(
+        test_data_name="nf1-data-nobarcode", test_dir_path=testing_dir
+    )
+
+    # Selecting one plate and meta data dir
+    plate = datafiles.plate_data[0]
+    metadata = datafiles.metadata
+
+    print(datafiles.barcode)
+
+    # execute
+    proc = subprocess.run(
+        f"cytosnake init -d {plate} -m {metadata}".split(),
+        capture_output=True,
+        text=True,
+        check=False,
+    )
+
+    # assert checks
+    assert proc.returncode == 0
+
+    # check generated files
+    test_utils.check_init_outputs(
+        paths=datafiles, test_dir=testing_dir, plate_data_ext="sqlite"
+    )
+
+
+@pytest.mark.postive
+def test_multiplates_with_multi_platemaps(testing_dir):
+    """Positive case test: Expects a 0 exit code
+
+    This test checks if the CLI can handle multiple plates and multiple plate maps
+    with a barcode as inputs.
+
+    checks for: data plates, data folder, cytosnake folder, barcodes in datafolder,
+    return code
+
+    Rational:
+    ---------
+        CytoSnake requires input from multiple platemaps and barcodes. To ensure
+        accurate mapping of plate data, it necessitates the use of a barcode as an
+        input. The barcode files are used by CytoSnake to correctly associate each
+        plate map with its corresponding plate data.
+
+    Parameters:
+    -----------
+    test_dir: pytest.fixture
+        Testing directory
+    """
+
+    # prepare testing files and select inputs
+    datafiles = test_utils.prepare_dataset(
+        test_data_name="nf1-data", test_dir_path=testing_dir
+    )
+    metadata = datafiles.metadata
+    barcode = datafiles.barcode
+
+    # execute CytoSnake in testing folder
+    proc = subprocess.run(
+        f"cytosnake init -d *.sqlite -m {metadata} -b {barcode}".split(),
+        capture_output=True,
+        text=True,
+        check=False,
+    )
+
+    # check subprocess execution
+    assert proc.returncode == 0
+
+    # check generated files
+    test_utils.check_init_outputs(
+        paths=datafiles, test_dir=testing_dir, plate_data_ext="sqlite"
+    )