Welcome to GPM’s documentation!

GPM (Genomic Project Manager) is a versatile command-line tool designed for managing and automating bioinformatic workflows.

Check out the Usage section for further information, including how to Installation the project.

Note

This project is under active development.

As next-generation sequencing (NGS) technologies continue to advance, the methodologies employed for processing and analyzing sequencing data have become increasingly diverse and are evolving at a rapid pace. This dynamic landscape poses significant challenges in project management, script reuse, and procedural documentation within the genomics community. Recognizing this need for adaptability and efficiency, the Genomic Pipeline Manager (GPM) has been meticulously designed to address these pressing issues and provide a robust solution for streamlining genomic analyses.

In the face of rapidly changing NGS technologies, project management can become complex due to the variety of data processing workflows and analysis tools available. GPM serves as a comprehensive solution by offering a centralized platform for managing and orchestrating diverse genomic projects. This includes facilitating the integration of cutting-edge methodologies, ensuring reproducibility, and promoting standardized practices across different sequencing experiments.

One of the key challenges in genomics research is the efficient reuse of analysis scripts. GPM tackles this issue by providing a structured framework for organizing and storing scripts, making them easily accessible for reuse across multiple projects. This not only enhances workflow efficiency but also promotes collaboration and knowledge sharing among researchers, fostering a more productive and interconnected genomics community.

Documentation is another critical aspect of genomic analyses, ensuring transparency, reproducibility, and the transfer of knowledge. GPM incorporates robust documentation features that allow researchers to capture and share detailed procedures, parameters, and outcomes associated with their analyses. This not only aids in project continuity but also provides an invaluable resource for researchers looking to replicate or build upon existing analyses.

In summary, GPM emerges as a pivotal tool in the genomics landscape, addressing the challenges posed by the rapid evolution of NGS technologies. By offering a centralized platform for project management, script reuse, and documentation, GPM empowers researchers to navigate the complexities of genomic analyses with efficiency, adaptability, and enhanced collaboration, ultimately advancing the field of genomics.

Contents

• Concept
  • One project.ini across all phases
  • Two levels of configuration files
  • Keeping everything in projects for reproducibility
  • Flexible addition of methods in any phase
• Usage
  • Installation
  • Configuration
  • nextflow.config
• How to
  • Demultiplex
  • Processing
  • Analysis
  • Export
  • Clean
  • Archive
• Customization
  • Customize your own config files
  • Customize your own author information
  • Customize your own institute information
• Development
  • Replaceable variables in template files
  • How to add a new demultiplexing method?
  • How to add a new processing method?
  • How to add a new analysis?

  _____                            _
 / ____|                          (_)
| |  __  ___ _ __   ___  _ __ ___  _  ___ ___
| | |_ |/ _ \ '_ \ / _ \| '_ ` _ \| |/ __/ __|
| |__| |  __/ | | | (_) | | | | | | | (__\__ \
 \_____|\___|_| |_|\___/|_| |_| |_|_|\___|___/
|  __ \         (_)         | |
| |__) | __ ___  _  ___  ___| |_
|  ___/ '__/ _ \| |/ _ \/ __| __|
| |   | | | (_) | |  __/ (__| |_
|_|  _|_|  \___/| |\___|\___|\__|
|  \/  |       _/ |
| \  / | __ _ |__/   __ _  __ _  ___ _ __
| |\/| |/ _` | '_ \ / _` |/ _` |/ _ \ '__|
| |  | | (_| | | | | (_| | (_| |  __/ |
|_|  |_|\__,_|_| |_|\__,_|\__, |\___|_|
                           __/ |
                          |___/