Scale data to unit variance and zero mean


ID: scale
Namespace: transform

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/scale/ \

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: "input.h5mu"
modality: "rna"
# max_value: 123.0
zero_center: true
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"

# 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/scale/ \
  -params-file params.yaml

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

Argument group


Name Description Attributes
--input Input h5mu file. file, required, example: "input.h5mu"
--modality List of modalities to process. string, default: "rna"
--max_value Clip (truncate) to this value after scaling. Does not clip by default. double
--zero_center If False, omit zero-centering variables, which allows to handle sparse input efficiently. boolean, default: TRUE
--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"


  • Dries Schaumont (maintainer)