HiC uniform processing pipeline

Directories

• backends/ : Backend configuration files (.conf)
• workflow_opts/ : Workflow option files (.json)
• examples/ : input JSON examples
• docker_image/ : Dockerfile
• nvidia_docker_image/ : Dockerfile for Nvidia Docker: to use pipeline with GPU
• test/ : test scripts for developers

Installation and tutorial

This pipeline supports many cloud platforms and cluster engines. It supports docker and singularity to resolve complicated software dependencies for the pipeline. A tutorial-based instruction for each platform will be helpful to understand how to run pipelines.

• Cloud platform (CLI)
  • Google Cloud Platform
• Stanford HPC server (CLI)
  • Stanford Sherlock 2.0 soon to be added
• Local Linux computers (CLI)
  • Local system with singularity
  • Local system with docker
• Cluster engines (CLI)
  • SLURM [partial documentation]

Input JSON file

Input JSON file specification [partial documentation]

Output directories

Output directory specification soon to be added