MRG: allow config to determine whether to run `gather` and `tax`

dib-lab / sourmash-slainte

Project template for sourmash-based characterization of genomes and metagenomes

BSD 3-Clause "New" or "Revised" License

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Closed ctb closed 7 months ago

ctb commented 7 months ago

run_gather in the config file now determines if the gather & tax steps are run.

This PR also:

moves most Python code from Snakefile to slainte_functions.py
removes table-reader plugin and uses mkdocs-macro & pandas to_markdown() instead