Combine one or more single-modality .h5mu files together into one .h5mu file


ID: merge
Namespace: dataflow

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/dataflow/merge/ \

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: ["sample_paths"]
# 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/dataflow/merge/ \
  -params-file params.yaml

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

Argument group


Name Description Attributes
--input Paths to the single-modality .h5mu files that need to be combined List of file, required, default: "sample_paths", multiple_sep: ","
--output Path to the output file. file, default: "output.h5mu"
--output_compression The compression format to be used on the output h5mu object. string, example: "gzip"


  • Dries Schaumont (maintainer)