INNUca-NF documentation!

INNUca-NF is a NextFlow implementation of the INNUENDO pipeline designed for the high quality assembly, quality control and annotation of bacterial genomes. As a NextFlow pipeline, it can be easily deployed in many computing environments with minimal requirements.

Requirements

• Java 8
• Docker
• NextFlow

Contents:

• generator package
  • Submodules
    • generator.HeaderSkeleton module
    • generator.Process module
  • Module contents
• nextflow_generator module
• templates package
  • Submodules
    • assembly_report module
    • fastqc module
    • fastqc_report module
    • integrity_coverage module
    • process_abricate module
    • process_assembly_mapping module
    • process_spades module
    • spades module
    • trimmomatic module
    • trimmomatic_report module
  • Module contents

Indices and tables

• Index
• Module Index
• Search Page