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Support for 10x FFPE scRNA #247

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pakiessling opened this issue Jul 3, 2023 · 5 comments · Fixed by #276
Closed

Support for 10x FFPE scRNA #247

pakiessling opened this issue Jul 3, 2023 · 5 comments · Fixed by #276
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@fmalmeida
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enhancement New feature or request

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@pakiessling
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Description of feature

Hi,
unsure if this is supported yet.
10x offers new kits to process scRNA from FFPE https://www.10xgenomics.com/products/single-cell-gene-expression-flex
The data is processed with cellranger multi https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi
It would be really cool to have this as part of the pipeline!
@pakiessling pakiessling added the enhancement New feature or request label Jul 3, 2023
@grst
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grst commented Jul 13, 2023

related discussion for adding cellranger multi:
#174

The cellranger multi module on nf-core/modules has been merged:
nf-core/modules#3229

@pakiessling
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@grst Cool. Does that mean I can use it in nf-core/scrnaseq yet or does the module still need to be incoperated?

@grst
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grst commented Jul 13, 2023

No, this still needs to be implemented here. I was just linking the issues for reference.

@grst grst mentioned this issue Oct 26, 2023
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@fmalmeida fmalmeida self-assigned this Nov 6, 2023
@grst grst mentioned this issue Jan 22, 2024
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@fmalmeida fmalmeida linked a pull request Feb 29, 2024 that will close this issue
Adding cellrangermulti subworkflow #276
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@fmalmeida
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Hi @grst ,
Should this ticket now be closed?

@grst
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grst commented May 23, 2024

Yes, this is now available with cellranger multi

@grst grst closed this as completed May 23, 2024
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Adding cellrangermulti subworkflow nf-core/scrnaseq
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@grst @fmalmeida @pakiessling