dataflow/move_anndata_slots

Description

Move slots (.obs, .var, .obsm, .varm, .obsp, .varp, .uns) from a modality
in a source MuData file into a modality in a target MuData file.
The specified slots are copied from the source modality into the target
modality. By default, copying to a key that already exists in the target
raises an error; use --allow_overwrite to overwrite it instead.

Type

python_script

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
source_modality: [ "rna" ]  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_composed.git \  
  -revision v0.2.0 \  
  -main-script target/nextflow/dataflow/move_anndata_slots/main.nf \  
  -params-file params.yaml

Source

Name	Type & Properties	Description
--input_source	file required	Source h5mu file to read slots from.
--source_modality	string	Modality in the source h5mu file to read slots from.

Name

Type & Properties

--input_source

file

required

--source_modality

string

Target

Name	Type & Properties	Description
--input_target	file required	Target h5mu file to write slots into.
--target_modality	string	Modality in the target h5mu file to write slots into. Defaults to the value of --source_modality.

Name

Type & Properties

--input_target

file

required

--target_modality

string

Slots to move

Name	Type & Properties	Description
--obs	string multiple	Column names from .obs to move from the source modality to the target modality. If not provided, .obs is not moved.
--var	string multiple	Column names from .var to move from the source modality to the target modality. If not provided, .var is not moved.
--obsm	string multiple	Keys from .obsm to move from the source modality to the target modality. If not provided, .obsm is not moved.
--varm	string multiple	Keys from .varm to move from the source modality to the target modality. If not provided, .varm is not moved.
--obsp	string multiple	Keys from .obsp to move from the source modality to the target modality. If not provided, .obsp is not moved.
--varp	string multiple	Keys from .varp to move from the source modality to the target modality. If not provided, .varp is not moved.
--uns	string multiple	Keys from .uns to move from the source modality to the target modality. If not provided, .uns is not moved.

Name

Type & Properties

--obs

string

multiple

--var

string

multiple

--obsm

string

multiple

--varm

string

multiple

--obsp

string

multiple

--varp

string

multiple

--uns

string

multiple

Options

Name	Type & Properties	Description
--allow_overwrite	boolean_true	Allow overwriting keys that already exist in the target modality. By default, the component raises an error if a key already exists. When enabled, existing keys are overwritten with a warning.

Name

Type & Properties

--allow_overwrite

boolean_true

Output

Name	Type & Properties	Description
--output -o	file required output	Output h5mu file (the target with slots added from the source).
--output_compression	string	Compression format to use for the output AnnData and/or Mudata H5 files. By default no compression is applied.

Name

Type & Properties

--output

-o

file

required

output

--output_compression

string