dataflow/concatenate_spatialdata

Description

Concatenate multiple SpatialData objects into one SpatialData output.

Type

python_script

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
anndata_join: [ "inner" ]  
anndata_pairwise: [ false ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/dataflow/concatenate_spatialdata/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--inputs	file required multiple	Paths to Zarr stores containing the SpatialData objects to concatenate.

Name

Type & Properties

--inputs

file

required

multiple

Outputs

Name	Type & Properties	Description
--output	file required output	The output Zarr store containing the concatenated SpatialData object.

Name

Type & Properties

--output

file

required

output

SpatialData options

Name	Type & Properties	Description
--attrs_merge	string	The method to use for merging elements in `attrs` when concatenating the SpatialData objects. See `anndata_merge` for options and details.

Name

Type & Properties

--attrs_merge

string

AnnData options

Name	Type & Properties	Description
--anndata_join	string	The type of join to perform on the AnnData objects when concatenating the main tables of the SpatialData objects: - "inner": Only variables (genes) that are present in all objects are kept. - "outer": All variables (genes) that are present in any object are kept. Sparse arrays are padded with zeros, other objects are filled with missing values. See `anndata.concat` for details.
--anndata_merge	string	The method to use for merging elements that are not aligned with `obs` when concatenating the main tables of the SpatialData objects: - None: No elements are kept. - "same": Only elements that are the same across all objects are kept. - "unique": Elements for which there is only one possible value are kept. - "first": The first element at each position is kept. - "only": Elements that are only in one object are kept. See `anndata.concat` for details.
--anndata_uns_merge	string	The method to use for merging elements in `uns` when concatenating the main tables of the SpatialData objects. See `anndata_merge` for options and details. Merging is applied recursively.
--anndata_label	string	The name of the column in `obs` of the concatenated main table to store batch label information. If not provided, no batch label column is added.
--anndata_pairwise	boolean	Whether pairwise elements (`obsp`/`varp`) are concatenated.

Name

Type & Properties

--anndata_join

string

--anndata_merge

string

--anndata_uns_merge

string

--anndata_label

string

--anndata_pairwise

boolean