dataset compress

Archive a QuantNado dataset directory or combined .zarr store as a tar.gz file.

The archive can be opened directly with QuantNado.open(...).

Usage

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

Required Options

• --dataset, --input: QuantNado dataset directory or combined .zarr store

Options

• --output, -o: output archive path; defaults to <dataset>.gz
• --overwrite / --no-overwrite: replace the output archive if it already exists
• --workers, --n-workers: number of pigz workers
• --log-file PATH: log destination
• --verbose, -v: debug logging

Notes

• with --workers > 1, pigz must be available in the runtime container
• with --workers 1, QuantNado can fall back to standard gzip if pigz is unavailable
• the output archive is a tar.gz archive even if the filename ends in .zarr.gz
• write the archive next to the dataset, not inside the dataset directory

Snakemake Example

shell:
    """
    quantnado dataset compress \
      --dataset {input.dataset:q} \
      --output {output.zipped_dataset:q} \
      --workers {threads} \
      --log-file {log:q}
    """