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the ability to specify --unknown-slide #99

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aguang opened this issue Dec 10, 2024 · 2 comments
Open

the ability to specify --unknown-slide #99

aguang opened this issue Dec 10, 2024 · 2 comments
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enhancement Improvement for existing functionality

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@aguang
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aguang commented Dec 10, 2024

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?

@aguang aguang added the enhancement Improvement for existing functionality label Dec 10, 2024
@fasterius
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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.

@fasterius
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fasterius commented Dec 20, 2024

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.

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