Split modalities

Split the modalities from a single .h5mu multimodal sample into seperate .h5mu files.

Info

ID: split_modalities
Namespace: dataflow

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/dataflow/split_modalities/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
input: # please fill in - example: "sample_path"
# output: "$id.$key.output.output"
# output_compression: "gzip"
# output_types: "$id.$key.output_types.csv"

# 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/dataflow/split_modalities/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	Path to a single .h5mu file.	file, required, default: "sample_path"
--output	Output directory containing multiple h5mu files.	file, required, example: "/path/to/output"
--output_compression	The compression format to be used on the output h5mu object.	string, example: "gzip"
--output_types	A csv containing the base filename and modality type per output file.	file, required, example: "types.csv"

Authors

• Dries Schaumont (maintainer)

• Robrecht Cannoodt (contributor)