flowcraft package

Subpackages

• flowcraft.generator package
  • Subpackages
    • flowcraft.generator.components package
      • Submodules
        • flowcraft.generator.components.annotation module
        • flowcraft.generator.components.assembly module
        • flowcraft.generator.components.assembly_processing module
        • flowcraft.generator.components.distance_estimation module
        • flowcraft.generator.components.downloads module
        • flowcraft.generator.components.metagenomics module
        • flowcraft.generator.components.mlst module
        • flowcraft.generator.components.patlas_mapping module
        • flowcraft.generator.components.reads_quality_control module
        • flowcraft.generator.components.typing module
      • Module contents
  • Submodules
    • flowcraft.generator.engine module
    • flowcraft.generator.error_handling module
    • flowcraft.generator.footer_skeleton module
    • flowcraft.generator.header_skeleton module
    • flowcraft.generator.inspect module
    • flowcraft.generator.pipeline_parser module
    • flowcraft.generator.process module
    • flowcraft.generator.process_details module
    • flowcraft.generator.recipe module
  • Module contents
• flowcraft.templates package
  • Subpackages
    • flowcraft.templates.flowcraft_utils package
      • Submodules
        • flowcraft.templates.flowcraft_utils.flowcraft_base module
      • Module contents
  • Submodules
    • flowcraft.templates.assembly_report module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • flowcraft.templates.fastqc module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • flowcraft.templates.fastqc_report module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • flowcraft.templates.integrity_coverage module
    • flowcraft.templates.mapping2json module
    • flowcraft.templates.mashdist2json module
      • Purpose
      • Expected input
      • Code documentation
    • flowcraft.templates.mashscreen2json module
    • flowcraft.templates.megahit module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • flowcraft.templates.metaspades module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • flowcraft.templates.pATLAS_consensus_json module
      • Purpose
      • Expected input
      • Code documentation
    • flowcraft.templates.pipeline_status module
      • Purpose
      • Expected input
      • Code documentation
    • flowcraft.templates.process_abricate module
    • flowcraft.templates.process_assembly module
    • flowcraft.templates.process_assembly_mapping module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • flowcraft.templates.skesa module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • flowcraft.templates.spades module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • flowcraft.templates.trimmomatic module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
    • flowcraft.templates.trimmomatic_report module
      • Purpose
      • Expected input
      • Generated output
      • Code documentation
  • Module contents
• flowcraft.tests package
  • Submodules
    • flowcraft.tests.data_pipelines module
    • flowcraft.tests.test_assemblerflow module
    • flowcraft.tests.test_engine module
    • flowcraft.tests.test_pipeline_parser module
    • flowcraft.tests.test_process_details module
    • flowcraft.tests.test_processes module
    • flowcraft.tests.test_sanity module
  • Module contents

Submodules

• flowcraft.flowcraft module

Module contents