This looks super cool, thanks for sharing @andrea.telatin! Do you have some examples of how you are currently using this tool in your own work?
I took a look at the
qax project README, and had a few things that I wanted to address:
accessing metadata in the artifacts requires the full Qiime2 installation
There actually isn’t any requirement that a “full QIIME 2 installation” is present in order to read QIIME 2 results. All results in QIIME 2 are saved in whatever their “normal format” is (BIOM, TSV, fastq.gz, etc) - and zipped into an Artifact or Visualization . The Archive specification that we have developed has a standard directory and file layout, as you have leveraged in your tool:
The exciting thing (to me) is that tools like
qax, q2view, or itol can all leverage the archive spec in order to parse the data and provenance for any QIIME 2-produced result.
not to mention that every release of Qiime2 will produce incompatible artifacts
This is not true - not only do new releases of QIIME 2 not necessarily produce new Archive Formats, but even if they do, backwards compatibility is always guaranteed! We have almost 25 releases of QIIME 2, and only 6 Archive formats. You can read a QIIME 2 2017.2 Artifact in QIIME 2 2020.8, pretty cool ! For a real-world example, check out this filtered feature table from the QIIME 2 docs:
It was imported using QIIME 2 2017.9, and then filtered using 2020.8!
100X times faster than Qiime2
You might get some questions about this - since QIIME 2 is an ecosystem of plugins and interfaces, you might want to qualify (and quantify) what you mean by “faster” in this case. Faster than
qiime tools peek?
Also, just a minor point, the project is called “QIIME 2” not “Qiime2,” as you have written in the README. As well, a citation or a link to the QIIME 2 project might be helpful, too, that way users will be able to get an idea of how your project fits into the broader ecosystem.
If you’re open to it, I would be happy to open PR against the
qax repo to start suggesting or providing some edits for the points raised above - just let me know!
Thanks again for sharing! This would be really great to get published up on the QIIME 2 Library soon, I will follow up with more details in the next few months!