cellgeni/nf-cluster

Introduction

cellgeni/nf-cluster is a Nextflow pipeline for single-cell ATAC processing from Cell Ranger ARC output directories to integrated clustering and visualization outputs.

The current ATAC workflow performs:

• AMULET doublet calling
• metadata attachment and QC filtering
• tile matrix generation and feature selection
• Scrublet doublet scoring
• on-disk concatenation across samples
• spectral embedding
• RAPIDS neighbors, Leiden clustering, and UMAP
• Scanpy embedding plots colored by Leiden and selected metadata columns

Usage

Prepare a sample sheet with the following columns:

sample,path
SAMPLE_A,/path/to/cellranger_arc_count_output_A
SAMPLE_B,/path/to/cellranger_arc_count_output_B

Each path should point to a Cell Ranger ARC output directory containing fragments files (for example, fragments.tsv.gz).

Run the ATAC workflow:

nextflow run cellgeni/nf-cluster \
   --input examples/samples.csv \
   --atac.genome hg38 \
   --outdir results

You can also provide parameters through a YAML/JSON params file:

nextflow run cellgeni/nf-cluster \
   -params-file params.yml

Key Parameters

• Required:
  • --input: CSV sample sheet with sample,path
  • --atac.genome: genome label used by the ATAC workflow
• Common:
  • --random_state
  • --outdir
• RAPIDS neighbors:
  • --neighbors.n_neighbors
  • --neighbors.algorithm
  • --neighbors.metric
  • --neighbors.method
• RAPIDS Leiden:
  • --leiden.resolution
  • --leiden.theta
  • --leiden.n_iterations
  • --leiden.key_added
• RAPIDS UMAP:
  • --umap.min_dist
  • --umap.spread
  • --umap.n_components
  • --umap.init_pos
• Embedding plotting:
  • --embeddingplot.basis (default: X_umap)
  • --embeddingplot.color (list, default includes leiden)
  • --embeddingplot.legend_loc

Output Overview

The pipeline writes linked outputs under the chosen outdir, including:

• h5ad/filtered: QC-filtered AnnData files
• h5ad/neighbors: AnnData with neighbor graph
• h5ad/leiden: AnnData with Leiden labels in obs
• h5ad/umap: AnnData with UMAP coordinates in obsm
• plots/embedding: PNG embedding plots (for example, UMAP colored by leiden)
• amulet: AMULET outputs
• reports: Nextflow execution report, timeline, trace, and DAG