Update directory structure & fix readme accordingly

karel-brinda / Phylign

Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)

http://brinda.eu/mof

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Closed karel-brinda closed 9 months ago

karel-brinda commented 9 months ago

Rename intermediate directories to follow the same naming patterns, which reflects the order of the individual steps of the pipeline
queries/ -> input/ to keep the same structure as in MiniPhy
Fix occasional formatting caused by the inability of snakefmt to correctly parse threads lambda functions (closes #240 )