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CHANGELOG.md

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# Changelog
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## [0.3.0] - 2021-07-09
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## [0.3.0] - 2021-07-12
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### Fixed
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- Refactor demultiplex.py for readability and faster execution
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- Logger is now compatible with snakemake logging module
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- Fixed small parsing bugs in gbk_convert.py
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### Changed
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- Remove third party folder which contained 'bowtie' executables
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- Remove third-party folder which contained `bowtie` executables (now `bowtie` is installed via conda or manually)
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- file paths are now handled by pathlib
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- New settings class that is compatible with snakemake
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- The map_reads script is now a stand-alone script
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- Settings class which is used by snakemake and pyinseq
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- Pyinseq and snakemake now use `pathlib` for handling filepaths
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- Removed readthedocs website
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- Pyinseq and snakemake now use `pathlib` for handling file paths
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- Removed readthedocs website (documentation is now in the README.md; no longer using ReadTheDocs)
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- Removed docs/
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- Removed third-party/
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### Added
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- Snakemake can now execute workflows using Snakefile in pyinseq
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- Additional Snakefiles for genomprep and demultiplex of pyinseq
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- Additional Snakefiles for genomeprep and demultiplex of pyinseq
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- Conda virtual environment files that allow conda to install `bowtie` software during runtime
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- Parser.py script for parsing command line arguments
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- Parser.py script for parsing command-line arguments
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- Include '--test' option for running pytest on pyinseq
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- New pytests for testing workflows in pyinseq
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- Pyinseq will now summarize sample information and snakemake output

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