Documentation for the REMIND-Cancer Filtering Pipeline

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Contents:

• Overview of the REMIND-Cancer Filtering Pipeline
  • Beyond Recurrence: A Novel Workflow to Identify Activating Promoter Mutations in Cancer Genomes
  • Abstract
  • Additional Repositories
  • Contact:
• Running the Pipeline: Technical Details and Implementation
  • General Overview
  • Details of Each Subfolder
    • 1. Utils
    • 2. Pipeline Setup
    • 3. Pipeline
• Validation / Pre-pipeline Scripts
  • 1. validate_configuration_file.py
    • Usage:
    • Checks Performed:
  • 2. validate_metadata_file.py
    • Usage:
    • Checks Performed:
  • 3. validate_rnaseq_dataframe.py
    • Usage:
    • Checks Performed:
  • General Notes
• Setting Up The Pipeline
  • Optional: Run Validation Scripts Before This
    • Validate Configuration File
    • Validate Metadata File
    • Validate RNA-Seq Dataframe
  • Usage
  • What This Script Does
    • 1. Load Configuration File
    • 2. Create Folder Structure for Patients
    • 3. Create a Results Tracking JSON
  • Detailed Breakdown of Functions
    • create_folder_structure(metadata_path, output_folder)
    • create_results_json(metadata_path, patient_folders_path, results_json_path)
    • main(config_path)
  • Expected Console Output
  • Prerequisites
  • Troubleshooting
• Manuscript: Figure Generation
• Examples: SNV and RNA-Seq Files