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AlexandrovLab / SigProfilerAssignment

Assignment of known mutational signatures to individual samples and individual somatic mutations

BSD 2-Clause "Simplified" License

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Development #131

Closed mdbarnesUCSD closed 4 months ago

mdbarnesUCSD commented 4 months ago

Added

Added CLI boolean handling to improve command-line interface usability.
Added new pytests for CLI to ensure correct handling of booleans.
Updated the README to reflect the new pytest additions.
Updated CI/CD pipelines to accommodate pytest changes.

Changed

Improved input_type value check mechanism to use .lower() before checking against values 'vcf' or 'matrix'.
Updated dependency from PyPDF2 to pypdf to increase compatibility and resolve installation issues on bioconda.

mdbarnesUCSD commented 4 months ago

closes #127