I wanted to share the QIIME 2 Provenance Replay paper, which was published last week in PLOS Computational Biology. You can find the article here.
If you haven't used QIIME 2's Provenance Replay functionality, now is a great time to try it out. If you're using QIIME 2 2023.9, it's already installed as part of your QIIME 2 environment. We have a brief tutorial on how to use it here.
Provenance Replay lets you generate new executable code (either a Python or shell script) from existing QIIME 2 Results (i.e., .qza or .qzv files). So if you have some Results around where you need to refresh yourself on how they were generated, or if you have results that someone shared with you and where you'd like to apply the same analysis on your data, try running the following command in your QIIME 2 environment:
qiime tools replay-supplement \
--in-fp my-qiime2-result.qzv \
Note: One caveat to be aware of is that all of the plugins that were used to create the result will need to be installed in the environment where you're calling
qiime tools replay-supplement. One that is frequently needed but not currently included in the amplicon distribution is rescript. If you run into an error that tells you No plugin currently registered with id: "rescript" (or some other plugin), that means you need to install that plugin in your environment. (Instructions for installing rescript can be found here, but we're currently working on resolving dependency conflicts to enable this to be installed in the QIIME 2 amplicon distribution.)
Enjoy replaying provenance!