jwg054000/RustPipe-SC

Full Pipeline

# H5AD input (Scanpy/nf-core output)
rustpipe-sc pipeline \
  --input sample.h5ad \
  --output results/ \
  --n-hvg 2000 --n-pcs 50 --knn-k 15

# 10x CellRanger H5 input
rustpipe-sc pipeline \
  --input filtered_feature_bc_matrix.h5 \
  --output results/ \
  --max-pct-mt 20.0

# CSV input
rustpipe-sc pipeline \
  --input expression.csv \
  --output results/

# Optional library QC from a Cell Ranger BAM (PATH rustqc; not the cell matrix)
rustpipe-sc pipeline \
  --input filtered_feature_bc_matrix.h5 \
  --output results/ \
  --qc-bam possorted_genome_bam.bam \
  --qc-gtf genes.gtf

Individual Steps

# QC metrics + cell filtering
rustpipe-sc qc --input raw.h5ad --output qc/ --min-genes 200 --max-pct-mt 5.0

# Normalize + log1p
rustpipe-sc normalize --input qc/filtered.csv --output norm/

# HVG selection (Seurat v3 method)
rustpipe-sc hvg --input norm/normalized.csv --output hvg/ --n-top-genes 2000

# PCA
rustpipe-sc pca --input hvg/expression_hvg.csv --output pca/ --n-components 50

# kNN graph
rustpipe-sc knn --input pca/pca_scores.csv --output knn/ --k 15

# Leiden clustering
rustpipe-sc leiden --input knn/knn.csv --output clusters/ --resolution 1.0

# Spatial autocorrelation (Moran's I)
rustpipe-sc morans-i \
  --input expression.csv \
  --coords spatial_coords.csv \
  --output spatial/

Global Options

--threads N    Number of threads (0 = all cores, default: 0)
--seed N       Random seed for reproducibility (default: 42)
-v/-vv/-vvv    Verbosity level