filter/subset_h5mu

Description

Create a subset of a mudata file by selecting the first number of observations

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 v3.0.0 \  
  -main-script target/nextflow/filter/subset_h5mu/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input	file required	Input h5mu file
--modality	string	Which modality from the input MuData file to process.
--output	file output	Output h5mu file.
--number_of_observations	integer	Number of observations to be selected from the 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

--input

file

required

--modality

string

--output

file

output

--number_of_observations

integer

--output_compression

string