Cellranger v9

[marcus-tutert]

Description of feature

Hi,

I was wondering if scrnaseq could be updated with cellranger version 9? Specifically because I would like to use the on-chip 10X GEM-X multiplexing options which I believe are needing v9 to be used
https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/inputs/cr-multi-config-csv-opts#samples

[grst]

Totally! If you want it fast, we'd encourage you to submit a pull request ;)

First step would be to update the module on nf-core/modules.

[marcus-tutert]

Thanks, I'll start a draft PR if that works for you @grst -- would be great to have you walk me through some of the technical bits :)

[apeltzer]

please also make sure to disable telemetry as a default - this is new in v9:

export TENX_DISABLE_TELEMETRY=1

[apeltzer]

Containers are there already, you may simply open up a PR and get to it 👍🏻

[apeltzer]

PR open, but you need to do the modules - please take over nf-core/modules#7153 :-)

[grst]

Status update on this: This is currently on hold because 10x doesn't want us (i.e. nfcore) to publish docker images with cellranger anymore. They promised to provide public container builds on their end, but this has not happend so far.

[grst]

We got another email from 10x, stating that we can go ahead hosting our own container again until they make their own one available.