Update bit-combine-bracken-and-add-lineage to allow users to pass a custom location for the taxonkit database

[sterrettJD]

Hey Mike, thanks for this nice toolkit :)

Recently, I've been wanting to use bit-combine-bracken-and-add-lineage without relying on the taxonkit database being stored in the root directory. Instead of the default ~/.taxonkit, I want users of a tool I'm developing to be able to place this in the working directory.

Maybe I'm missing a better way to do this, but I updated bit-combine-bracken-and-add-lineage to accommodate this, and it worked for me. Users can now pass various paths for this database, and it defaults to ~/.taxonkit if nothing is passed.

I did this by adding an argument -d to the script, then passing that to the taxonkit --data-dir argument.

Let me know what you think about this approach and if you'd be interested in incorporating this in the toolkit. Happy to make some adjustments if needed.

Thanks,
John

[AstrobioMike]

awesome! Looks clean and straightforward to me, I'll merge and update the conda version :)

thanks, John!