Make zarr store chunking and sharding configurable via CLI

[Copilot]

Chunking and sharding for intermediate OME-Zarr stores were hardcoded in snakebids.yml. This exposes them as CLI options and wires them into the workflow at runtime.

Changes

• snakebids.yml: Adds two new CLI args; removes hardcoded chunks from zarrnii_out_kwargs.storage_options:
  • --zarr-store-chunks — 4-int tuple (c, x, y, z), default 1 128 128 128
  • --zarr-store-shards — 4-int tuple (c, x, y, z), default disabled
• Snakefile: Reads both CLI values and populates config['zarrnii_out_kwargs']['storage_options'] at startup; sharding is suppressed when --zarr-store-ext ozx (zip format doesn't support sharding)

Example

# Custom chunks, no shards (ozx format — shards silently ignored even if provided)
spimquant bids/ out/ participant --zarr-store-chunks 1 256 256 256

# Enable sharding (requires ome.zarr directory format)
spimquant bids/ out/ participant \
  --zarr-store-ext ome.zarr \
  --zarr-store-chunks 1 128 128 128 \
  --zarr-store-shards 1 512 512 512