--- a
+++ b/scripts/analyse_cic.py
@@ -0,0 +1,96 @@
+import argparse
+import os
+import subprocess
+import sys
+import yaml
+import papermill as pm
+
+sys.path.append('.')
+sys.path.append('..')
+
+from pyMultiOmics.common import create_if_not_exist
+
+
+def load_config_file(config_file):
+    with open(config_file) as f:
+        config = yaml.safe_load(f)
+    return config
+
+
+def main(args):
+
+    # input excel
+    input_excel = os.path.abspath(args.input_excel)
+    print('Input Excel:', input_excel)
+
+    # annotation CSV
+    annot_csv = os.path.abspath(args.annot_csv)
+    print('Annotation CSV:', annot_csv)
+
+    # config file
+    config_file = os.path.abspath(args.config_file)
+    print('Config file:', config_file)
+    processing_params = load_config_file(config_file)
+
+    print('Pre-processing parameters:')
+    print(yaml.dump(processing_params, indent=4))
+    params = {}
+    params['file_name'] = input_excel
+    params['annot_csv'] = annot_csv
+    params.update(processing_params)
+
+    # output dir
+    output_dir = os.path.abspath(args.output_dir)
+    print('Output Directory:', output_dir)
+
+    # Check if template file exists in parent directory
+    template_parent_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
+    template_file = os.path.abspath(
+        os.path.join(template_parent_dir, 'templates', 'cic_template.ipynb'))
+
+    if os.path.isfile(template_file):
+        print('Template Notebook:', template_file)
+    else:
+        # Check if template file exists in current directory
+        template_file = os.path.abspath(os.path.join('.', 'templates', 'cic_template.ipynb'))
+
+        if os.path.isfile(template_file):
+            print('Template Notebook:', template_file)
+        else:
+            print('Error: template notebook not found')
+            return
+
+    output_notebook = os.path.abspath(os.path.join(output_dir, 'cic_analysis.ipynb'))
+    output_pdf = os.path.abspath(os.path.join(output_dir, 'cic_analysis.pdf'))
+
+    print('Output Notebook:', output_notebook)
+    print('Output PDF:', output_pdf)
+
+    create_if_not_exist(output_dir)
+    _ = pm.execute_notebook(template_file, output_notebook, report_mode=True, parameters=params)
+
+    command = ['jupyter', 'nbconvert', '--TemplateExporter.exclude_input=True', '--output',
+               output_pdf,
+               '--to', 'pdf', output_notebook]
+    result = subprocess.run(command, capture_output=True, text=True)
+
+    if result.returncode == 0:
+        print(f'\nPDF output saved to {output_pdf}\n')
+    else:
+        print(f'\nFailed to create PDF: {result.stderr}\n')
+
+
+if __name__ == '__main__':
+    print('***********************************')
+    print('* CIC Analysis                    *')
+    print('***********************************')
+    print()
+
+    parser = argparse.ArgumentParser(
+        description='Runs a notebook-based analysis on input data and saves the results as a PDF.')
+    parser.add_argument('--input_excel', required=True, help='Path to the input Excel file.')
+    parser.add_argument('--annot_csv', required=True, help='Path to the annotation CSV file.')
+    parser.add_argument('--output_dir', required=True, help='Path to the output directory.')
+    parser.add_argument('--config_file', required=True, help='Path to the YAML configuration file.')
+    args = parser.parse_args()
+    main(args)