Disclaimer: I’m pretty new to using Qiime 2, and am slowly modifying directions from the Tutorials to suit my own data analysis needs. So somethings that might be obvious to the “seasoned Qiime-2” community are still in the exponential growth phase of my own learning curve…
Something that might be improved to help other newbs: I noticed an issue in the “Available Plugins” page under Qiime 2017.8 that caused much head-scratching…
While trying to modify the denoise-paired script provided under the DADA2 section of the “Atacama Soils Tutorial” using the denoise-paired detail page under “Available Plugins” I ran into two separate issues:
- It took me a while to figure out that --i and --p and --o refer to the Input, Parameter and Output “headings” of the table respectively - it might be useful to indicate this somewhere so people who are new to Qiime 2 scripting “language”
- All the “options” for Parameters have underscores between the words (e.g. “n_threads” to change the number of cores available) but when you add this command to run in qiime, it must be “n-threads” with a hyphen (like all the other commands in the tutorial), NOT an underscore (which none of the commands in the tutorial use). This should definitely be fixed in the documentation (unless there’s some reason to include underscores when you really need hyphens?)… That way us newbs can start to massage the analysis workflow to better suit our own needs…
Thanks!