First off, big congrats on the release of qiime 2018.4 ! With the ever growing number of options and branches of the available pipelines I was thinking it might now be useful to have an annotation option when creating artifacts. For example:
qiime feature-table rarefy \
--p-sampling-depth 2000 \
--o-rarefied-table rarefied-table.qza \
--comment "2000 depth drops S02 & S04 only, could increase to 7000 at a cost of losing S05 and S07 also"
This would just allow the user to keep track of their thought process when revisiting an analyses, leave notes for revisions, explanatory comments when sharing it with a colleague, or simply describe what is in the artifact if for some reason they’ve forgotten and can’t remember from the filename.
I imagine a simple text file in the artifacts would suffice to call on, but even better if it can be integrated into the provenance flowchart somehow.
Looking forward to everyone’s thoughts.
This is indeed a great idea. There have been several instances where I have forgotten or misplaced my notes on the reasoning behind why I had performed or applied certain settings in my analyses. It’d be great to leave notes like this for example: “I filtered my OTU according to Bokulich et al., 2013” or “I am extracting the amplicon region from my reference sequences for more robust taxonomy assignment as per Werner et al., 2012”.