Hi, I'm using 2020.8 and I've noticed when I run align-to-tree-mafft-fasttree, the trees are generated, but the output-dir command is not working properly. The directory gets created, but the tree files end up in the current working directory. I'm not sure if this is a bug or if it's something I'm doing, so I thought I'd ask here.
Hey there @rhizorick, let's take a closer look at the help text for the --output-dir flag:
--output-dir PATH Output unspecified results to a directory
So what that is saying, is any results that aren't explicitly specified should be saved into the directory specified here. You are specifying all 4 of the outputs here:
so, there are no unspecified outputs by the time we get to the --output-dir flag.
I see two potential solutions.
One, you can manually make the output dir yourself, and specify the output paths into that dir: