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Option to use the `--unknown-slide` parameter in `spaceranger count`

Open pstorozenko opened this issue 7 months ago • 0 comments

Description of feature

Hi! Thanks for the work on the pipeline! I wonder if you ever considered adding the possibility to add the --unknown-slide parameter to the spaceranger count in the spatialvi pipeline?

Current design doesn't allow for it, and expects the slide and area parameters to be always present, not allowing to work with visium-1/2/2-large data.

https://github.com/nf-core/spatialvi/blob/f846f0031f3b0e4fd344324cf4ef4d1404583683/modules/nf-core/spaceranger/count/main.nf#L34-L50

Best!

pstorozenko avatar Jul 03 '24 09:07 pstorozenko