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NationalGenomicsInfrastructure/ngi_pipeline

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ngi_pipeline/engines/piper_ngi/workflows.py

Summary

Maintainability
B
6 hrs
Test Coverage

Function workflow_dna_variantcalling has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

def workflow_dna_variantcalling(qscripts_dir_path, setup_xml_path,
                                config, exec_mode, output_dir=None, *args, **kwargs):
    """Return the command line for DNA Variant Calling.

    :param strs qscripts_dir_path: The path to the Piper qscripts directory.
Severity: Minor
Found in ngi_pipeline/engines/piper_ngi/workflows.py - About 1 hr 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 return_cl_for_workflow has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

def return_cl_for_workflow(workflow_name, qscripts_dir_path, setup_xml_path,
Severity: Major
Found in ngi_pipeline/engines/piper_ngi/workflows.py - About 1 hr to fix

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

    def workflow_genotype_concordance(qscripts_dir_path, setup_xml_path,
    Severity: Major
    Found in ngi_pipeline/engines/piper_ngi/workflows.py - About 50 mins to fix

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

      def workflow_dna_variantcalling(qscripts_dir_path, setup_xml_path,
      Severity: Major
      Found in ngi_pipeline/engines/piper_ngi/workflows.py - About 50 mins to fix

        Similar blocks of code found in 3 locations. Consider refactoring.
        Open

            try:
        workflow_function = getattr(sys.modules[__name__], workflow_fn_name)
    except AttributeError as e:
        error_msg = "Workflow \"{}\" has no associated function.".format(workflow_fn_name)
        LOG.error(error_msg)
        Severity: Major
        Found in ngi_pipeline/engines/piper_ngi/workflows.py and 2 other locations - About 2 hrs to fix
        ngi_pipeline/engines/piper_ngi/parsers.py on lines 15..20
        ngi_pipeline/engines/qc_ngi/workflows.py on lines 31..36

        Duplicated Code

        Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

        Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

        When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

        Tuning

        This issue has a mass of 54.

        We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

        The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

        If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

        See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

        Refactorings

        Further Reading

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