Log1p

Logarithmize the data matrix.

Info

ID: log1p
Namespace: transform

Links

Source

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

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -main-script target/nextflow/transform/log1p/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
input: # please fill in - example: "input.h5mu"
modality: "rna"
# input_layer: "foo"
# output_layer: "foo"
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"
# base: 2

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -profile docker \
  -main-script target/nextflow/transform/log1p/main.nf \
  -params-file params.yaml

Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument group

Arguments

Name	Description	Attributes
--input	Input h5mu file	file, required, example: "input.h5mu"
--modality		string, default: "rna"
--input_layer	Input layer to use. If None, X is normalized	string
--output_layer	Output layer to use. By default, use X.	string
--output	Output h5mu file.	file, required, default: "output.h5mu"
--output_compression	The compression format to be used on the output h5mu object.	string, example: "gzip"
--base		double, example: 2

Authors

• Dries De Maeyer (maintainer)

• Robrecht Cannoodt (contributor)