I am trying to find the version of specific packages used in the qiime2 plugins, in order to report what versions I used. For example, the version of dada2, cutadapt, and scikit-learn used. I know that
qiime info gives you version numbers, but most of these look like the same version of qiime that I had used (2020.2) and are only for the plugins (not for any other packages). I used
qiime tools citations as well on my taxonomy.qza file, and that doesn't tell me the version of scikit-lean. The version info I see is (among other citations) feature-classifier:2020.2.0, dada2:2020.2.0 and cutadapt:2020.2.0.
I am using qiime in a conda environment, so I looked up the packages and versions in that conda environment with
conda list. With this, I can see that it is cutadapt version 2.8, but there is also q2-cutadapt version 2020.2.0. Which one would be the correct one to report? The only dada2 I can see is q2-dada2 version 2020.2.0. This versioning doesn't look like the way the versions are listed on the dada2 webpage current version is 1.16? Is this because it is a qiime2 version of dada2 (not the R version)? But isn't there a specific version of dada2 (version 1.x) used in qiime2 (and has changed over time, as I've seen in forum posts)? How can I find this version information? Or is 2020.2.0 sufficient to report for dada2 managed in qiime2 now?
I can find the version of scikit-learn using the conda list command (version 0.22.1). But is there a way to find this information more easily?
Sorry there are a lot of questions in there. Really, I want to be able to say that we used qiime 2 version 2020.2, primers were trimmed using cutadapt version x, denoising was done with dada2 version y, and ASVs were classified using scikit learn version z. And I'm having trouble with what those versions actually are.