Log1p

Logarithmize the data matrix.

Info

ID: log1p
Namespace: transform

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 0.12.6 -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 0.12.6 -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)