assemblerflow package

Subpackages

• assemblerflow.generator package
  • assemblerflow.generator.components package
    • Submodules
      • assemblerflow.generator.components.annotation module
      • assemblerflow.generator.components.assembly module
      • assemblerflow.generator.components.assembly_processing module
      • assemblerflow.generator.components.distance_estimation module
      • assemblerflow.generator.components.downloads module
      • assemblerflow.generator.components.mapping module
      • assemblerflow.generator.components.reads_quality_control module
    • Module contents
  • Submodules
    • assemblerflow.generator.engine module
    • assemblerflow.generator.error_handling module
    • assemblerflow.generator.header_skeleton module
    • assemblerflow.generator.pipeline_parser module
    • assemblerflow.generator.process module
    • assemblerflow.generator.process_details module
  • Module contents
• assemblerflow.templates package
  • Subpackages
    • assemblerflow.templates.utils package
      • Submodules
        • assemblerflow.templates.utils.assemblerflow_base module
      • Module contents
  • Submodules
    • assemblerflow.templates.assembly_report module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • assemblerflow.templates.fastqc module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • assemblerflow.templates.fastqc_report module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • assemblerflow.templates.integrity_coverage module
      • Purpose
      • Expected input
      • Generated output
      • Notes
      • Code documentation
    • assemblerflow.templates.mapping2json module
      • Purpose
      • Expected input
      • Code documentation
    • assemblerflow.templates.mashdist2json module
      • Purpose
      • Expected input
      • Code documentation
    • assemblerflow.templates.mashscreen2json module
      • Purpose
      • Expected input
      • Code documentation
    • assemblerflow.templates.pATLAS_consensus_json module
      • Purpose
      • Expected input
      • Code documentation
    • assemblerflow.templates.pipeline_status module
      • Purpose
      • Expected input
      • Code documentation
    • assemblerflow.templates.process_abricate module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • assemblerflow.templates.process_assembly_mapping module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • assemblerflow.templates.process_spades module
    • assemblerflow.templates.spades module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • assemblerflow.templates.trimmomatic module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • assemblerflow.templates.trimmomatic_report module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
  • Module contents
• assemblerflow.tests package
  • Submodules
    • assemblerflow.tests.test_processes module
    • assemblerflow.tests.test_sanity module
  • Module contents

Submodules

• assemblerflow.assemblerflow module

Module contents