nft-anndata

nf-test plugin for AnnData stores in .h5ad and .zarr formats.

Note: As of v0.3.3, nft-anndata is a lightweight wrapper around nf-anndata. The core reading logic is maintained there and pulled in as a git submodule. nft-anndata automatically inherits all fixes and new features from nf-anndata releases.

Features

• n_vars and n_obs dimensions
• Dataframes (obs and var)
  • Column names and row names
  • Named, integer, and unnamed indices
  • Per-column data access (all numeric types, categorical, boolean, nullable, string)
  • Unique values and unique count per column
• Keys of available fields in layers, obsm, varm, obsp, varp, uns
• Sparse and dense X matrix support
• Chunked and compressed HDF5 dataset support for .h5ad
• AnnData-on-Zarr v2 directory store support for .zarr

Examples can be found here.

Architecture

nft-anndata provides two nf-test integration points:

• anndata(path) — global function callable in any then {} block
• path(file).anndata() — extension on nf-test's path() object

Both return an AnnData instance from nf-anndata, which does the actual .h5ad or .zarr parsing.