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...

That is a fair point, however charliecloud in nf-core is currently broken irrespective of these changes. I think adding this now and providing a config for people who want to...

Thanks for approving, `charliecloud.registry` is actually still broken in 24.03.0-edge. I figured out how it is done now, see here https://github.com/nextflow-io/nextflow/pull/5018

Any comments or thoughts on this PR?

Any chance someone could review this and let me know if anything should be changed or done differently before this can be merged? @pditommaso @bentsherman