I like to keep a centralized singularity cache for all the modules instead of having it in my home dir. I am the only user and admin of the hardware, but that might change at some point. So that centralized location is owned by root and permissions can't be changed without sudo, but otherwise the directory is set up with read-write-execute for everyone. No module should have any issue using it.

Indeed, all the pipeline steps run fine... until it gets to salmon quant (with or without STAR) and there it crashes because it cannot change permissions to the cache directory. Never any other step, always salmon quant.

I thought it was a new issue in 3.20, but 3.14 also behaves that way. In the past apparently I had "solved" it by giving myself ownership of that centralized directory, but it recently resurfaced when, not remembering why I owned the dir, I gave it back to root.

This behaviour of the salmon module makes no sense to me. I feel this qualifies as a bug, but I am clueless about the inner workings of the module to confidently label it as such.