@Matthias Zepper and @Jonathan Manning This is with regards to this pull https://github.com/nf-core/rnaseq/pull/1672 From my perspective, I'm happy with this -- I only use rsem when I'm using the pipeline for human samples, and in that case I want to apply the encode settings. My concern was with how to set those since

extra_star_align_args

can't be used with

star_rsem

. But the encode settings are applied by default when with

star_rsem

, so all that was necessary was highlighting that in the docs. @Matthias Zepper thinks that the

extra_star_align_args

might be valid for

star_rsem

, however, and suggested moving the conversation here. That particular option isn't something that I personally need -- I think that if manipulating the star settings is necessary, then requiring

star_salmon

is fine. But I do like accurate documentation, so if anyone has thoughts on how to make the docs as accurate as possible I'm happy to keep revising the details around this.

I just responded to @mashehu on #C06TPECB95H . Most of this comes from my caution- I just moved the STAR process outside of RSEM and wanted to keep thing mostly stable otherwise. If others want to test and verify that things work without the the current warnings/ restrictions, I'd be content to strip them.

whoops, forgot about the dev channels. moving there

Wrong Matthias tagged, I think 😉

I would also always go for the most competent, if I had a choice 😉

sorry Matthiases!

did you meant @Matthias De Smet?

I know nothing!

That is something...and from Socrates.

And John Snow