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NationalGenomicsInfrastructure/ngi_pipeline

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ngi_pipeline/engines/piper_ngi/command_creation_config.py

Summary

Maintainability
A
3 hrs
Test Coverage

Function build_setup_xml has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

def build_setup_xml(project, sample, workflow, local_scratch_mode, config):
    """Build the setup.xml file for each project using the CLI-interface of
    Piper's SetupFileCreator.

    :param NGIProject project: The project to be converted.
Severity: Minor
Found in ngi_pipeline/engines/piper_ngi/command_creation_config.py - About 2 hrs to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function build_piper_cl has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

def build_piper_cl(project, workflow_name, setup_xml_path, exit_code_path,
Severity: Major
Found in ngi_pipeline/engines/piper_ngi/command_creation_config.py - About 50 mins to fix

    Function build_setup_xml has 5 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def build_setup_xml(project, sample, workflow, local_scratch_mode, config):
    Severity: Minor
    Found in ngi_pipeline/engines/piper_ngi/command_creation_config.py - About 35 mins to fix

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