From h5ad to h5mu

Converts a single layer h5ad file into a single MuData object

Info

ID: from_h5ad_to_h5mu
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 0.12.6 -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 0.12.6 -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)