atx_convert¶

At a glance

Repository: atlasxomics/atx_convert · Display name: atx_convert · Modality: Epigenomics · Stage: Helper Workflow

Overview¶

A single-step Workflow for converting ATX epigenomics objects between formats — AnnData (.h5ad), Seurat (.rds), and BPCells directories. It lets analysts move data between the Python (Scanpy/SnapATAC2) and R (Seurat/ArchR) ecosystems, optionally carrying spatial coordinates across.

Provide one source (anndata_file, seurat_file, or bpcells_dir); the Workflow converts it to the complementary format.

Steps¶

convert_task — Detects the supplied source and runs the matching converter (to_seurat.R, from_seurat.R, from_bpcells.R, …), optionally copying spatial coordinates and/or emitting a converted_sm.h5ad. Outputs are written under latch:///converted/<output_directory>/.

Inputs¶

Parameter	Type	Description
`output_directory`	str	Output subdirectory under `converted/`.
`anndata_file`	LatchFile	`.h5ad` AnnData object from an ATX experiment.
`seurat_file`	LatchFile	`.rds` Seurat object from an ATX experiment.
`seurat_spatial`	bool	Copy spatial coordinates to the new object (default `True`).
`seurat_clean`	bool	Also emit `converted_sm.h5ad` (a smaller / cleaned object).
`bpcells_dir`	LatchDir	Directory containing a Seurat object backed by BPCells.
`bpcells_spatial`	bool	Copy spatial coordinates (BPCells source).
`bpcells_clean`	bool	Emit `converted_sm.h5ad` (BPCells source).

Outputs¶

A LatchDir under latch:///converted/<output_directory>/. Which files appear depends on the conversion direction:

converted/<output_directory>/
├── converted.h5ad  or  converted.rds        # per conversion direction
├── converted_sm.h5ad                        # when "Convert to _sm"
├── converted_bp.h5ad, converted_bp_sm.h5ad  # BPCells source
├── obs.csv
├── metadata.csv
└── reductions.txt

File	Description
`converted.h5ad`	AnnData produced from a Seurat or BPCells source.
`converted.rds`	Seurat object produced from an AnnData source.
`converted_sm.h5ad`	Reduced "`_sm`" AnnData — only when Convert to `_sm` is enabled.
`converted_bp.h5ad` / `converted_bp_sm.h5ad`	AnnData (and reduced variant) produced from a BPCells directory.
`obs.csv`, `metadata.csv`, `reductions.txt`	Cell metadata, object metadata, and the dimensionality-reduction names carried across.

Example run¶

(Representative LaunchPlan / batch-table example to be added.)