transform/clr

Description

Perform CLR normalization on CITE-seq data (Stoeckius et al., 2017).

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: [ "prot" ]  
output: "$id.$key.output"  
axis: [ 0 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.0 \  
  -main-script target/nextflow/transform/clr/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--modality	string	Which modality from the input MuData file to process.
--output -o	file required output	Output h5mu file.
--input_layer	string	Input layer to use. By default, .X is used.
--output_layer	string	Output layer to use. By default, use X.
--axis	integer	Axis across which CLR is performed. If set to 0, CLR is performed across observations (cells). If set to 1, CLR is performed across features (genes).
--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

-i

file

required

--modality

string

--output

-o

file

required

output

--input_layer

string

--output_layer

string

--axis

integer

--output_compression

string