metadata/move_obsm_to_obs

Description

Move a matrix from .obsm to .obs. Newly created columns in .obs will
be created from the .obsm key suffixed with an underscore and the name of the columns
of the specified .obsm matrix.

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

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

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.2 \  
  -main-script target/nextflow/metadata/move_obsm_to_obs/main.nf \  
  -params-file params.yaml

MuData Input

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--modality	string	Which modality from the input MuData file to process.
--obsm_key	string required	Key of a data structure to move from `.obsm` to `.obs`.

Name

Type & Properties

--input

-i

file

required

--modality

string

--obsm_key

string

required

MuData Output

Name	Type & Properties	Description
--output -o	file required output	Output h5mu file.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--output

-o

file

required

output

--output_compression

string