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You're right, this is currently not included in the pipeline, although it does seem like this is more something that should get included in the spaceranger/count module itself rather than the spatialvi pipeline. I will see what I can do regarding this.
A PR to the spaceranger/count module is up (see link above), but will likely not be merged until after the holidays are over (see a Slack thread here: https://nfcore.slack.com/archives/CJRH30T6V/p1734510282197769). In the meantime, you can always change the module code yourself according to the PR, if you're keen to start using the functionality, @aguang.
Description of feature
It doesn't seem like with the nextflow pipeline that there is a way to specify
--unknown-slide
(as described here: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/inputs/image-slide-parameters) as an option instead of--slide
and--area
. If there is a way to do so, could you point me to it? And if not, can this be implemented as a feature given that it's a space ranger option?The text was updated successfully, but these errors were encountered: