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- Also adjust bullet indentation
Also see https://snakemake.readthedocs.io/en/stable/snakefiles/best_practices.html for advice; mainly, it is simpler to just write paths than to assemble them using a 'WORK_DIR' variable, and use functions in params to extract paths from input and output files
Other changes: - Update parallel command - Correct merging CRISPRidentify batches - Correctly integrate script with Snakemake variables
This includes: - Move databases to 'resources' - Move output to 'results' Other changes: - Download databases automatically - Have Snakemake check for missing input - should fix #7 - Apply snakefmt
This includes: - Separate downloading of PhageScope and PLSDB (2 scripts instead of 1) Bugfixes: - Add end message to bin/prepare_genomes.sh - Add parallel to 'basic' env
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Prepare for release 0.2. Code overhaul and a number of bugfixes. Implement some of Snakemake's best practices for code quality, readability and portability and reproducibility. This will force a complete rerun of your analyses!
Documentation has not been updated and needs revision of many parts. (Planned for version 0.4.)
Feature updates
resources/for databases andresults/for outputall_atb_files.tsvBugfixes/code cleanup:
Fixes: #7, #24. Partly solves #19.