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Command-Line Interface

QuantNado exposes a dataset command group plus call-peaks:

Command Purpose
dataset create Build one per-sample .zarr store from direct assay inputs
dataset combine Merge per-sample .zarr stores into one multi-sample dataset
dataset compress Archive a QuantNado dataset as a tar.gz file
call-peaks Call peaks from a QuantNado dataset

Global Help

quantnado --help
quantnado --version

Current CLI Model

  • dataset create is per-sample and input-file-driven
  • outputs are written as one .zarr store per sample
  • dataset combine accepts one --stores flag followed by a list of store paths
  • dataset compress writes tar.gz archives that QuantNado.open(...) can read directly
  • test-mode builds can use either the default chromosome trio or repeated --test-chrom values
  • call-peaks works from QuantNado zarr inputs, not from bigWig directories

Typical Workflow

quantnado dataset create \
  --sample ATAC_1 \
  --assay ATAC \
  --bamfile /data/ATAC_1.bam \
  --output-dir dataset

quantnado dataset combine \
  --stores dataset/ATAC_1.zarr dataset/RNA_1.zarr \
  --output dataset/combined.zarr

quantnado dataset compress \
  --dataset dataset/combined.zarr \
  --output dataset/combined.zarr.gz \
  --workers 8

quantnado call-peaks \
  --zarr dataset/combined.zarr \
  --method quantile \
  --output-dir peaks

More Detail