transform/log1p

Description

Logarithmize the data matrix. Computes X = log(X + 1), where log denotes the natural logarithm unless a different base is given.

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"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/transform/log1p/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.
--input_layer	string	Input layer to use. If None, X is normalized
--output_layer	string	Output layer to use. By default, use X.
--output -o	file required output	Output h5mu file.
--base	double	Base of the logarithm. Natural logarithm is used by default.
--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

--input

-i

file

required

--modality

string

--input_layer

string

--output_layer

string

--output

-o

file

required

output

--base

double

--output_compression

string