Use of Configuration File in QIIME 2

Hello Everybody!

As I was running some diversity analyses, I noticed that the plugin includes a --cmd-config option, yet I could not much information on what parameters can be passed through this file, and how the file should be formatted. Thank you in advance for the help!

Sirtaj Singh :whale2:

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Hi @Sirtaj-Singh! Good eye - cmd-config is an undocumented option in q2cli. It is a supported flag in all plugins, on all Methods and Visualizers.

I am unsure if it will remain a feature of the cli interface in the future - it provides a lot of the same functionality as a generic shell script. For now, if it is something you are interested in playing with a bit more, this might get you started:

$ qiime demux summarize --cmd-config my-awesome-analysis.ini
$ qiime dada2 denoise-single --cmd-config my-awesome-analysis.ini

And an example of what my-awesome-analysis.ini might look like:

[demux.summarize]
i-data=demux.qza
o-visualization=demux.qza

[dada2.denoise-single]
i-demultiplexed-seqs=demux.qza
p-trunc-len=120
o-table=table.qza
o-representative-sequences=rep-seqs.qza

Let us know if that gets you moving, thanks! :t_rex:

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