Inconsistent default protocol

[martinkim0]

Description of the bug

Currently, nextflow_schema.json lists 10XV2 as the default protocol, so that is what is displayed in the docs. However, it looks like 10XV3 is actually the default being used as seen in nextflow.config.

Command used and terminal output

No response

Relevant files

No response

System information

nf-core/scrnaseq dev

[grst]

And it should actually be removed from both and be part of the samplesheet, s.t. protocol can bet set on a per-sample basis.

I thought this was implemented long time ago, but probably it never was? @fmalmeida, @apeltzer?

@ameynert removed the protocol from the test samplesheet in nf-core/test-datasets@fdd2d2b. Did I miss something (maybe during the hackathon) or was it just not implemented and therefore removed from the samplesheet to not be misleading?

[apeltzer]

Guess that was not implemented but would have to dig myself what in the end was (not) done.

[grst]

Fixed in dev. The default protocol is now "auto" for 10x.