From h5ad to h5mu

Converts a single layer h5ad file into a single MuData object

Info

ID: from_h5ad_to_h5mu
Namespace: convert

Links

Source

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/convert/from_h5ad_to_h5mu/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
input: # please fill in - example: ["input.h5ad"]
modality: ["rna"]
# 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/convert/from_h5ad_to_h5mu/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 h5ad files	List of file, required, default: "input.h5ad", multiple_sep: ";"
--modality		List of string, default: "rna", multiple_sep: ";"
--output	Output MuData file.	file, default: "output.h5mu"
--output_compression		string, example: "gzip"

Authors

• Dries De Maeyer (maintainer)