KwanLab / Autometa

Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
https://autometa.readthedocs.io
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Change arg name `--norm-output` for `autometa-kmers` entrypoint #310

Open chasemc opened 1 year ago

chasemc commented 1 year ago

Don't change this yet, but the following argument name is confusing. It's an input path to a tsv of normalized kmer counts but is named norm-output.

https://github.com/KwanLab/Autometa/blob/baf61c04dddf5b33bb825dba2841de1e38dffefe/autometa/common/kmers.py#L736-L740

The command's output file path is also named ...-output: https://github.com/KwanLab/Autometa/blob/baf61c04dddf5b33bb825dba2841de1e38dffefe/autometa/common/kmers.py#L758-L762

chasemc commented 1 year ago

I'm making a couple edits to this file elsewhere, so wait until those are merged before addressing this

evanroyrees commented 1 year ago

NOTE: These are both input and outputs paths. If the paths do not exist, autometa-kmers will write the respective files to the specified paths.