Niklas Schandry

I guess I should have said 'works, although it is not a great idea' :). I think using `--write-fake` for upcoming versions is the best solution, the main issue I...

I generally agree that breaking backwards compatibility could be justified in this case. I see the issues of the multi-user cache.. In practice that cache is pretty much only used...

To sum up: I think the fact that relying on `--write-fake` would break compatibility with older kernels is very problematic. Not supporting older charliecloud versions is one thing, but dropping...

I could not reproduce the "stale file handle" outside nextflow, it might also have other, filesystem related reasons. > Processes on the same node that are in different containers cannot...

Hi, similar to @jdwinkler-lanzatech I would be interested in being able to use non-prodigal gene calls or annotations. Following the discussion here, I took a look at GeneProfile.py and I...

Hi Matt, Thanks for getting back to me. Using prodigal for inStrain works very well. Currently I am adding in the annotations later on during analysis, which works fine for...