CholGen / bacpage

Snakemake pipeline for analysis of pathogen genomes. Will be pathogen-agnostic in the future but is currently designed for *Vibrio Cholerae*
GNU General Public License v3.0
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Rename phylogeny output from .tree to .nwk #1

Open dpark01 opened 8 months ago

dpark01 commented 8 months ago

bacpage phylogeny emits a newick-formatted file called phylogeny.tree. While some downstream programs are fine with consuming things ending in .tree, others (notably auspice.us) would prefer they end in .nwk or .newick (microreact seems fine with .tree though). Having users rename files as part of a normal analysis workflow can be a bit error prone / unnecessary, could be better to emit a file extension that maximizes out-of-the-box usage by downstream tools.