https://github.com/cellgeni/hackathon

https://github.com/cellgeni/hackathon

Last synced: 5 months ago
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• Host: GitHub
• URL: https://github.com/cellgeni/hackathon
• Owner: cellgeni
• Created: 2025-05-28T02:06:22.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2025-11-27T19:53:38.000Z (7 months ago)
• Last Synced: 2025-11-30T04:25:40.294Z (7 months ago)
• Language: Python
• Size: 12.6 MB
• Stars: 0
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# Hackaton pipeline

Running the pipeline:

```bash

sample_sheet="example/sample_sheet.csv"

metadata="example/metadata_splited.csv"

embedding="example/projection.csv"

delimiter="_"

nextflow run main.nf \

    --sample_sheet "$sample_sheet" \

    --metadata "$metadata" \

    --delimiter "__" \

    --method "umap" \

    --vis_label "celltype" \

    --embedding $embedding \

    --embedding_name "tsne" \

    -resume

```