Welcome to RattleSNP’s documentation!

Best SNP calling workflow

About RattleSNP

• From fastq to bam
  • Mapping
  • Optional statistics
• SNP calling
• Filter VCF and genetics tools

Install

• Requirements
• Install RattleSNP PyPI package
• Steps for LOCAL installation
  • install_local
• Steps for HPC distributed cluster installation
  • install_cluster
  • 1. Adapt profile and cluster_config.yaml
  • 2. Adapt tools_path.yaml
• Check install
  • test_install
• Advance installation
  • 1. Snakemake profiles
  • 2. Adapting cluster_config.yaml
  • 3. How to configure tools_path.yaml
  • And more …

Defining Workflows

• How to create a workflow
  • create_config
  • 1. Providing data
  • 2. Providing params
  • 3. Provide workflow step
  • 4. Parameters for some specific tools
• How to run the workflow
  • run_cluster
  • run_local
• Advance run
  • Providing more resources
  • Providing your own tools_config.yaml
• Output on RattleSNP
• Report

Project Info

• Citation
• License

FAQ

• Frequently Asked Questions

API

• rattleSNP
  • create_config
  • edit_cluster_config
  • edit_tools
  • install_cluster
  • install_local
  • run_cluster
  • run_local
  • test_install

Indices and tables

• Index

• Module Index

• Search Page