Performs Harmony integration based as described in https://github.com/immunogenomics/harmony.


ID: harmonypy
Namespace: integrate

Based on an implementation in python from https://github.com/slowkow/harmonypy

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/integrate/harmonypy/main.nf \

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: "path/to/file"
# output: "$id.$key.output.output"
# output_compression: "gzip"
modality: "rna"
obsm_input: "X_pca"
obsm_output: "X_pca_integrated"
theta: [2]
obs_covariates: # please fill in - example: ["batch", "sample"]

# 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/integrate/harmonypy/main.nf \
  -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
--output Output h5mu file. file, required
--output_compression The compression format to be used on the output h5mu object. string, example: "gzip"
--modality string, default: "rna"
--obsm_input Which .obsm slot to use as a starting PCA embedding. string, default: "X_pca"
--obsm_output In which .obsm slot to store the resulting integrated embedding. string, default: "X_pca_integrated"
--theta Diversity clustering penalty parameter. Specify for each variable in group.by.vars. theta=0 does not encourage any diversity. Larger values of theta result in more diverse clusters. List of double, default: 2, multiple_sep: ":"
--obs_covariates The .obs field(s) that define the covariate(s) to regress out. List of string, required, example: "batch", "sample", multiple_sep: ":"


  • Dries Schaumont (maintainer)

  • Robrecht Cannoodt (contributor)