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!
Hi @Sirtaj-Singh! Good eye -
cmd-config is an undocumented option in
q2cli. It is a supported flag in all plugins, on all
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:
Let us know if that gets you moving, thanks!
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