Welcome to RAFT’s documentation!

RAFT (Reproducible Analyses Framework and Tools) is a Python wrapper for Nextflow DSL2 that allows users to easily run common bioinformatics workflow while providing complete control of workflow behaviors.

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

Note

This project is under active development.

Contents

• Installation
  • Prerequisites
  • Installing through Conda
  • Installing through pip
  • Setup
• Manifest
  • Manifest purpose
  • Sample, patient, and dataset heirarchy
  • Manifest contents
• Usage
  • Quick Start
  • Finding Off-the-shelf Workflows
  • Running Off-the-shelf Workflows
  • Running Off-the-shelf Workflows with User-defined Parameters
• Outputs
  • reports/
  • Hierarchical Output Directory Structure
  • samples/
  • qc/
• Modules
  • Available modules
  • Module design strategy
    • Tool-level modules
    • Thematic modules
      • RAFT workflows are generic
      • RAFT workflows are nested
  • Generic workflows with specific tools
    • Tool and parameter string parsing
    • Conditional execution
  • Adding new tools to a generic workflow
  • Creating new generic workflows
    • Workflow syntax and relationships among nested workflows
  • Module interdependence
• Off-the-shelf workflows
  • Repository organization
  • Configuring off-the-shelf workflows
    • Off-the-shelf configuration file
    • JSON workflow description file
      • modules
      • steps
      • references
      • references_postproc
      • find_and_replace