Hi Spatialvi team, thank you for working on this pipeline! Is it possible to pin the Space Ranger version when running the spatialvi pipeline? For example, I want to use Space Ranger v2.1.0 instead of the current v3.1.3 to replicate a paper's result. Thanks!

Hi, Zoey! You can do this by supplying your own config file (using

-c <path/to/config>

) and changing the version of the Docker image, like so:

process {
  withName: SPACERANGER_COUNT {
    container = '<image>'
}

The default quay.io images (https://quay.io/repository/nf-core/spaceranger?tab=tags) used by nf-core are only built for versions

3.0.0

,

3.1.2

,

3.1.3

and

4.0.1

, but there are older versions over on DockerHub (https://hub.docker.com/r/nfcore/spaceranger/tags), including

2.1.0

.

Thank you for pointing out the Docker image!!

You're very welcome, hope it works out