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0.3.0: Snakemake and conda compatibility, updated documentation, code refactoring
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@eburgoswisc eburgoswisc released this 13 Jul 00:36
· 15 commits to master since this release
v0.3.0
8057e31

[0.3.0] - 2021-07-12

Fixed

  • Refactor demultiplex.py for readability and faster execution
  • Logger is now compatible with snakemake logging module
  • Fixed small parsing bugs in gbk_convert.py

Changed

  • Remove third-party folder which contained bowtie executables (now bowtie is installed via conda or manually)
  • file paths are now handled by pathlib
  • New settings class that is compatible with snakemake
  • The map_reads script is now a stand-alone script
  • Settings class which is used by snakemake and pyinseq
  • Pyinseq and snakemake now use pathlib for handling file paths
  • Removed readthedocs website (documentation is now in the README.md; no longer using ReadTheDocs)
  • Removed docs/
  • Removed third-party/

Added

  • Snakemake can now execute workflows using Snakefile in pyinseq
  • Additional Snakefiles for genomeprep and demultiplex of pyinseq
  • Conda virtual environment files that allow conda to install bowtie software during runtime
  • Parser.py script for parsing command-line arguments
  • Include '--test' option for running pytest on pyinseq
  • New pytests for testing workflows in pyinseq
  • Pyinseq will now summarize sample information and snakemake output
  • New user guide for pyinseq
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