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gustaveroussy / sopa

Technology-invariant pipeline for spatial omics analysis (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / ...) that scales to millions of cells
https://gustaveroussy.github.io/sopa/
BSD 3-Clause "New" or "Revised" License
123 stars 14 forks source link

Add nextflow pipeline #7

Open quentinblampey opened 10 months ago

quentinblampey commented 10 months ago

The snakemake pipeline should be translated to nextflow to reach more users. Don't hesitate to comment this issue to show your interest, else we keep it as a low priority

EDIT: I'm not very familiar to Nextflow, so I'm open to pull requests :)

jeffquinn-msk commented 4 months ago

We wrote a nextflow pipeline for running baysor on 10X Xenium in case its helpful: https://github.com/tansey-lab/nuc2seg/blob/main/nextflow/workflows/nf-core/baysor/main.nf

quentinblampey commented 4 months ago

Thanks @jeffquinn-msk, I'll have a look!