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module zarp

Main class and entry point when imported as a library.

Global Variables

  • config
  • utils
  • version
  • plugins
  • abstract_classes
  • samples
  • snakemake
  • runner
  • zarp
  • models

class ZARP

Handle ZARP workflow execution.

Args:

  • config: ZARP-cli configuration.

Attributes:

  • config: ZARP-cli configuration.

method __init__

__init__(config: Config)

Class constructor.


method execute_run

execute_run(samples: SampleRecordProcessor)  None

Execute run.

Args:

  • samples: Sample record processor instance.

method process_samples

process_samples()  SampleRecordProcessor

Process samples.

Returns: Sample record processor instance.


method set_up_run

set_up_run()  None

Set up run.

Raises:

  • FileNotFoundError: If genome assemblies map file is not found.