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ngi_pipeline/engines/qc_ngi/workflows.py

Summary

Maintainability
D
1 day
Test Coverage

Function workflow_fastq_screen has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

def workflow_fastq_screen(input_files, output_dir, config):
    # Get the path to the fastq_screen command
    fastq_screen_path = config.get("paths", {}).get("fastq_screen")
    if not fastq_screen_path:
        if find_on_path("fastq_screen", config):
Severity: Minor
Found in ngi_pipeline/engines/qc_ngi/workflows.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 workflow_fastqc has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

def workflow_fastqc(input_files, output_dir, config):
    """The constructor of the FastQC command line.

    :param list input_files: The list of fastq files to analyze (may be 2D for read pairs)
    :param str output_dir: The path to the desired output directory (will be created)
Severity: Minor
Found in ngi_pipeline/engines/qc_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 fastq_to_be_analysed has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

def fastq_to_be_analysed(fastq_files, analysis_dir, output_footers):
    """Produces a list of couples, the first element is the file itself, the second is the name of the soflink to be created.

    :param list fastq_files: The list of fastq files to analyze
    :param str analysis_dir: the folder where the analysis results will be stored
Severity: Minor
Found in ngi_pipeline/engines/qc_ngi/workflows.py - About 55 mins 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_cls_for_workflow has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

def return_cls_for_workflow(workflow_name, input_files, output_dir, config=None, config_file_path=None):
Severity: Minor
Found in ngi_pipeline/engines/qc_ngi/workflows.py - About 35 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/qc_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/piper_ngi/workflows.py on lines 65..70

    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

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

        if cl_list:
        safe_makedir(output_dir)
        # Module loading
        modules_to_load = get_all_modules_for_workflow("fastq_screen", config)
        mod_list = [ "module load {}".format(module) for module in modules_to_load ]
    Severity: Major
    Found in ngi_pipeline/engines/qc_ngi/workflows.py and 1 other location - About 2 hrs to fix
    ngi_pipeline/engines/qc_ngi/workflows.py on lines 111..117

    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 52.

    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

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

        if cl_list:
        safe_makedir(output_dir) #create the fastqc folder as fastqc wants it and I have to create soflinks
        # Module loading
        modules_to_load = get_all_modules_for_workflow("fastqc", config)
        mod_list = [ "module load {}".format(module) for module in modules_to_load ]
    Severity: Major
    Found in ngi_pipeline/engines/qc_ngi/workflows.py and 1 other location - About 2 hrs to fix
    ngi_pipeline/engines/qc_ngi/workflows.py on lines 178..184

    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 52.

    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

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

        if not fastq_screen_path:
        if find_on_path("fastq_screen", config):
            LOG.info("fastq_screen found on PATH")
            fastq_screen_path = "fastq_screen"
        else:
    Severity: Major
    Found in ngi_pipeline/engines/qc_ngi/workflows.py and 1 other location - About 1 hr to fix
    ngi_pipeline/engines/qc_ngi/workflows.py on lines 79..84

    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 39.

    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

    Similar blocks of code found in 2 locations. Consider refactoring.
    Open

        if not fastqc_path:
        if find_on_path("fastqc", config):
            LOG.info("fastqc found on PATH")
            fastqc_path = "fastqc"
        else:
    Severity: Major
    Found in ngi_pipeline/engines/qc_ngi/workflows.py and 1 other location - About 1 hr to fix
    ngi_pipeline/engines/qc_ngi/workflows.py on lines 126..131

    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 39.

    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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