Enable user specification of rank in filter_taxa.rule

dahak-metagenomics / dahak-taco

🌮 Taco is an experimental command line interface for dahak workflows. https://dahak-metagenomics.github.io/dahak-taco

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

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Enable user specification of rank in filter_taxa.rule #1

Closed brooksph closed 6 years ago

brooksph commented 6 years ago

@kternus pointed out that the current protocol generates reports at the genus rank with -r genus. We should enable the user to choose any taxonomic rank in the the taxonomic classification workflow by modifying the filter_taxa.rule.

brooksph commented 6 years ago

Same functionality should be enabled in the kaiju2krona.rule

charlesreid1 commented 6 years ago

Great! Thanks for the feedback! Since workflow steps share a lot of the same parameters, I've moved all parameters for a given workflow into a single .settings file, so it's a one-stop place to see what configuration options a user has. So, I'll add a taxonomic_rank option to taxonomic_classification.settings

charlesreid1 commented 6 years ago

By the way, I should mention that organizing things into .rule and .settings files makes it pretty trivial to convert any hard-coded argument into a user-defined argument. For example, here's the commit where I added the taxonomic_rank option. It only took 3 lines! (well, 5 including {}s):

Commit: 7e00ddf2e3a5883a9f7e5eb8e7378d99d44b932b