From h5mu to h5ad

Converts a h5mu file into a h5ad file


ID: from_h5mu_to_h5ad
Namespace: convert

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 0.12.0 -latest \
  -main-script target/nextflow/convert/from_h5mu_to_h5ad/ \

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: "input.h5mu"
modality: "rna"
# output: "$id.$key.output.h5ad"
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 0.12.0 -latest \
  -profile docker \
  -main-script target/nextflow/convert/from_h5mu_to_h5ad/ \
  -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 MuData file file, required, default: "input.h5mu"
--modality string, default: "rna"
--output Output AnnData file. file, default: "output.h5ad"
--output_compression The compression format to be used on the final h5ad object. string, default: "gzip"


  • Robrecht Cannoodt (maintainer)